PARADIGM pathway analysis of mRNASeq expression data
Bladder Urothelial Carcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1JD4VHR
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1JD4VHR
Overview
Introduction

PAthway Representation and Analysis by Direct Inference on Graphical Models (PARADIGM) predicts the activity of a diverse set of molecular concepts such as genes, complexes, and processes. The predicted activities are called Inferred Pathway Levels (IPLs) and are derived from a probabilistic belief propagation strategy that incorporates multimodal data such as copy number and gene expression estimates with a concept's pathway context.

Summary

There were 64 significant pathways identified in this analysis.

Table 1.  Get Full Table Top 10 out of 131 pathways in order of significance.

Pathway.Name Avg.Num.Perturbations
FOXM1 transcription factor network 93
Glypican 2 network 71
Aurora B signaling 64
Signaling events regulated by Ret tyrosine kinase 58
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 52
Signaling mediated by p38-alpha and p38-beta 47
Signaling events mediated by the Hedgehog family 46
Nongenotropic Androgen signaling 44
IL4-mediated signaling events 43
Endothelins 43
Results
Summary Table

The following list describes the columns found in Table 2.

  • Pathway.Name = Full pathway name of curated PARADIGM pathway

  • Significance.Ratio = (Ave.Num.Perturbations)/ (Cohort Size) where Cohort Size is 267 . Pathway is significant if Significance.Ratio > 0.05 .

  • Avg.Num.Perturbations = Average number of samples with perturbations across the pathway concepts determined by a background permutation model (>2 standard deviations away from the permuted distribution)

  • Total.Perturbations = Total number of perturbed concepts across all samples (>2 standard deviations away from the permuted distribution)

  • Num.Entities = Number of concepts that belong to the pathway

  • Min.Mean.Truth = Minimum IPL for concepts in the pathway among real samples

  • Max.Mean.Truth = Maximum IPL for concepts in the pathway among real samples

  • Min.Mean.Within = Minimum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Max.Mean.Within = Maximum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Min.Mean.Any = Minimum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes)

  • Max.Mean.Any = Maximum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes).

Table 2.  Get Full Table This summary table provides a report of cancer type specific pathway perturbations. Click on the links in the first column to display more detailed results for each pathway. A pathway is defined as significant (red number in Significance.Ratio column) if the Ave.Num.Perturbationsis > 5% of the cohort size ( 267 ).

Pathway.Name Significance.Ratio Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
FOXM1 transcription factor network 0.3483 93 4747 51 -0.81 0.015 1000 -1000 -0.14 -1000
Glypican 2 network 0.2659 71 287 4 -0.14 -0.11 1000 -1000 -0.012 -1000
Aurora B signaling 0.2397 64 4349 67 -0.5 0.015 1000 -1000 -0.055 -1000
Signaling events regulated by Ret tyrosine kinase 0.2172 58 4759 82 -0.28 0.015 1000 -1000 -0.069 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1948 52 3553 68 -0.69 0.35 1000 -1000 -0.086 -1000
Signaling mediated by p38-alpha and p38-beta 0.1760 47 2070 44 -0.24 0.015 1000 -1000 -0.042 -1000
Signaling events mediated by the Hedgehog family 0.1723 46 2409 52 -0.18 0.18 1000 -1000 -0.044 -1000
Nongenotropic Androgen signaling 0.1648 44 2292 52 -0.24 0.13 1000 -1000 -0.046 -1000
IL4-mediated signaling events 0.1610 43 3984 91 -0.79 0.55 1000 -1000 -0.11 -1000
Endothelins 0.1610 43 4163 96 -0.32 0.053 1000 -1000 -0.059 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.1573 42 3353 78 -0.28 0.1 1000 -1000 -0.044 -1000
IGF1 pathway 0.1498 40 2287 57 -0.25 0.049 1000 -1000 -0.078 -1000
Reelin signaling pathway 0.1386 37 2112 56 -0.22 0.039 1000 -1000 -0.072 -1000
p75(NTR)-mediated signaling 0.1348 36 4503 125 -0.16 0.045 1000 -1000 -0.079 -1000
Aurora C signaling 0.1348 36 255 7 -0.21 0 1000 -1000 -0.024 -1000
TCGA08_retinoblastoma 0.1348 36 294 8 -0.23 0.063 1000 -1000 -0.014 -1000
Thromboxane A2 receptor signaling 0.1311 35 3714 105 -0.19 0.036 1000 -1000 -0.054 -1000
HIF-1-alpha transcription factor network 0.1236 33 2540 76 -0.33 0.033 1000 -1000 -0.054 -1000
PLK1 signaling events 0.1236 33 2814 85 -0.35 0.049 1000 -1000 -0.041 -1000
Plasma membrane estrogen receptor signaling 0.1236 33 2859 86 -0.25 0.13 1000 -1000 -0.066 -1000
Ephrin A reverse signaling 0.1161 31 219 7 -0.071 0 1000 -1000 -0.014 -1000
Fc-epsilon receptor I signaling in mast cells 0.1161 31 3099 97 -0.18 0.04 1000 -1000 -0.069 -1000
IL23-mediated signaling events 0.1161 31 1891 60 -0.61 0.015 1000 -1000 -0.12 -1000
Ras signaling in the CD4+ TCR pathway 0.1161 31 527 17 -0.15 0.021 1000 -1000 -0.027 -1000
Syndecan-1-mediated signaling events 0.1124 30 1044 34 -0.27 0.015 1000 -1000 -0.029 -1000
Rapid glucocorticoid signaling 0.1124 30 601 20 -0.23 0.035 1000 -1000 -0.018 -1000
Integrins in angiogenesis 0.1086 29 2489 84 -0.27 0.031 1000 -1000 -0.075 -1000
Glypican 1 network 0.1049 28 1356 48 -0.26 0.035 1000 -1000 -0.03 -1000
PDGFR-alpha signaling pathway 0.1049 28 1242 44 -0.32 0.032 1000 -1000 -0.045 -1000
amb2 Integrin signaling 0.1049 28 2328 82 -0.33 0.021 1000 -1000 -0.061 -1000
BMP receptor signaling 0.1011 27 2218 81 -0.31 0.051 1000 -1000 -0.069 -1000
Glucocorticoid receptor regulatory network 0.1011 27 3162 114 -0.6 0.26 1000 -1000 -0.066 -1000
TCR signaling in naïve CD8+ T cells 0.1011 27 2590 93 -0.14 0.065 1000 -1000 -0.065 -1000
Calcium signaling in the CD4+ TCR pathway 0.1011 27 838 31 -0.28 0.015 1000 -1000 -0.075 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0974 26 1371 52 -0.3 0.03 1000 -1000 -0.035 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0974 26 3155 120 -0.33 0.19 1000 -1000 -0.059 -1000
S1P1 pathway 0.0936 25 912 36 -0.29 0.016 1000 -1000 -0.047 -1000
LPA receptor mediated events 0.0936 25 2606 102 -0.23 0.033 1000 -1000 -0.067 -1000
IL6-mediated signaling events 0.0936 25 1911 75 -0.24 0.068 1000 -1000 -0.058 -1000
S1P5 pathway 0.0899 24 413 17 -0.16 0.11 1000 -1000 -0.02 -1000
Visual signal transduction: Cones 0.0824 22 858 38 -0.12 0.018 1000 -1000 -0.052 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0824 22 1189 54 -0.19 0.03 1000 -1000 -0.081 -1000
LPA4-mediated signaling events 0.0787 21 252 12 -0.17 0.022 1000 -1000 -0.018 -1000
IL12-mediated signaling events 0.0787 21 1828 87 -0.4 0.029 1000 -1000 -0.092 -1000
BCR signaling pathway 0.0787 21 2086 99 -0.19 0.035 1000 -1000 -0.074 -1000
S1P4 pathway 0.0787 21 543 25 -0.16 0.029 1000 -1000 -0.028 -1000
Wnt signaling 0.0749 20 144 7 -0.057 0.015 1000 -1000 -0.015 -1000
S1P3 pathway 0.0749 20 857 42 -0.16 0.03 1000 -1000 -0.021 -1000
Coregulation of Androgen receptor activity 0.0712 19 1484 76 -0.22 0.034 1000 -1000 -0.035 -1000
Osteopontin-mediated events 0.0712 19 727 38 -0.18 0.016 1000 -1000 -0.082 -1000
JNK signaling in the CD4+ TCR pathway 0.0712 19 336 17 -0.15 0.017 1000 -1000 -0.029 -1000
TCGA08_p53 0.0712 19 139 7 -0.16 0.073 1000 -1000 -0.009 -1000
Arf6 signaling events 0.0674 18 1139 62 -0.24 0.029 1000 -1000 -0.048 -1000
Aurora A signaling 0.0674 18 1121 60 -0.35 0.029 1000 -1000 -0.042 -1000
Class IB PI3K non-lipid kinase events 0.0674 18 54 3 -0.024 -1000 1000 -1000 -0.012 -1000
Syndecan-2-mediated signaling events 0.0637 17 1198 69 -0.086 0.034 1000 -1000 -0.027 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0599 16 549 34 -0.047 0.015 1000 -1000 -0.046 -1000
FAS signaling pathway (CD95) 0.0599 16 789 47 -0.57 0.019 1000 -1000 -0.034 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0599 16 1467 88 -0.24 0.057 1000 -1000 -0.082 -1000
Presenilin action in Notch and Wnt signaling 0.0562 15 947 61 -0.18 0.043 1000 -1000 -0.056 -1000
Syndecan-4-mediated signaling events 0.0562 15 1048 67 -0.18 0.022 1000 -1000 -0.07 -1000
Noncanonical Wnt signaling pathway 0.0524 14 373 26 -0.092 0.015 1000 -1000 -0.036 -1000
Canonical Wnt signaling pathway 0.0524 14 763 51 -0.18 0.081 1000 -1000 -0.04 -1000
Visual signal transduction: Rods 0.0524 14 741 52 -0.2 0.015 1000 -1000 -0.074 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0487 13 388 28 -0.16 0.03 1000 -1000 -0.023 -1000
ErbB4 signaling events 0.0449 12 880 69 -0.23 0.036 1000 -1000 -0.072 -1000
Effects of Botulinum toxin 0.0449 12 334 26 -0.074 0.015 1000 -1000 -0.05 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0449 12 416 33 -0.28 0.044 1000 -1000 -0.037 -1000
ErbB2/ErbB3 signaling events 0.0412 11 779 65 -0.23 0.026 1000 -1000 -0.055 -1000
Caspase cascade in apoptosis 0.0412 11 820 74 -0.049 0.044 1000 -1000 -0.026 -1000
Regulation of Androgen receptor activity 0.0412 11 770 70 -0.22 0.03 1000 -1000 -0.058 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0375 10 876 85 -0.21 0.022 1000 -1000 -0.065 -1000
IL27-mediated signaling events 0.0375 10 517 51 -0.24 0.025 1000 -1000 -0.062 -1000
IL2 signaling events mediated by STAT5 0.0375 10 230 22 -0.12 0.062 1000 -1000 -0.02 -1000
Hedgehog signaling events mediated by Gli proteins 0.0337 9 609 65 -0.16 0.064 1000 -1000 -0.049 -1000
FOXA2 and FOXA3 transcription factor networks 0.0337 9 452 46 -0.18 0.095 1000 -1000 -0.039 -1000
Nectin adhesion pathway 0.0337 9 601 63 -0.048 0.03 1000 -1000 -0.055 -1000
EGFR-dependent Endothelin signaling events 0.0337 9 202 21 -0.061 0.022 1000 -1000 -0.06 -1000
Regulation of nuclear SMAD2/3 signaling 0.0300 8 1115 136 -0.18 0.067 1000 -1000 -0.053 -1000
Cellular roles of Anthrax toxin 0.0300 8 318 39 -0.095 0.018 1000 -1000 -0.019 -1000
IL1-mediated signaling events 0.0300 8 502 62 -0.095 0.073 1000 -1000 -0.081 -1000
IL2 signaling events mediated by PI3K 0.0300 8 500 58 -0.18 0.049 1000 -1000 -0.063 -1000
a4b1 and a4b7 Integrin signaling 0.0262 7 38 5 -0.006 0.007 1000 -1000 -0.013 -1000
Signaling events mediated by PTP1B 0.0262 7 600 76 -0.14 0.036 1000 -1000 -0.065 -1000
Ephrin B reverse signaling 0.0262 7 351 48 -0.051 0.02 1000 -1000 -0.051 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0262 7 586 83 -0.27 0.042 1000 -1000 -0.061 -1000
Syndecan-3-mediated signaling events 0.0262 7 274 35 -0.14 0.045 1000 -1000 -0.035 -1000
Regulation of p38-alpha and p38-beta 0.0262 7 392 54 -0.15 0.039 1000 -1000 -0.045 -1000
Class I PI3K signaling events mediated by Akt 0.0225 6 431 68 -0.21 0.059 1000 -1000 -0.042 -1000
Ceramide signaling pathway 0.0225 6 501 76 -0.25 0.044 1000 -1000 -0.033 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0225 6 238 37 -0.033 0.035 1000 -1000 -0.038 -1000
Signaling events mediated by HDAC Class III 0.0225 6 278 40 -0.22 0.025 1000 -1000 -0.033 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0225 6 461 74 -0.25 0.075 1000 -1000 -0.076 -1000
Regulation of Telomerase 0.0225 6 657 102 -0.16 0.04 1000 -1000 -0.083 -1000
Insulin Pathway 0.0225 6 455 74 -0.26 0.041 1000 -1000 -0.075 -1000
BARD1 signaling events 0.0187 5 318 57 -0.15 0.045 1000 -1000 -0.055 -1000
IFN-gamma pathway 0.0187 5 358 68 -0.17 0.055 1000 -1000 -0.078 -1000
EPHB forward signaling 0.0187 5 431 85 -0.041 0.04 1000 -1000 -0.076 -1000
Signaling events mediated by PRL 0.0187 5 199 34 -0.094 0.026 1000 -1000 -0.029 -1000
E-cadherin signaling events 0.0187 5 28 5 -0.004 0.017 1000 -1000 -0.015 -1000
EPO signaling pathway 0.0150 4 266 55 -0.046 0.052 1000 -1000 -0.078 -1000
TRAIL signaling pathway 0.0150 4 232 48 -0.01 0.048 1000 -1000 -0.054 -1000
Signaling mediated by p38-gamma and p38-delta 0.0150 4 67 15 0 0.032 1000 -1000 -0.025 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0150 4 193 45 -0.031 0.068 1000 -1000 -0.076 -1000
Arf6 trafficking events 0.0150 4 339 71 -0.41 0.049 1000 -1000 -0.059 -1000
PDGFR-beta signaling pathway 0.0150 4 454 97 -0.056 0.058 1000 -1000 -0.072 -1000
PLK2 and PLK4 events 0.0112 3 10 3 0.006 0.019 1000 -1000 -0.009 -1000
Retinoic acid receptors-mediated signaling 0.0112 3 230 58 -0.086 0.035 1000 -1000 -0.061 -1000
Paxillin-dependent events mediated by a4b1 0.0112 3 120 36 -0.033 0.034 1000 -1000 -0.058 -1000
TCGA08_rtk_signaling 0.0112 3 102 26 -0.072 0.045 1000 -1000 -0.016 -1000
E-cadherin signaling in the nascent adherens junction 0.0112 3 260 76 -0.019 0.056 1000 -1000 -0.07 -1000
Signaling events mediated by HDAC Class II 0.0075 2 205 75 -0.087 0.038 1000 -1000 -0.036 -1000
Class I PI3K signaling events 0.0075 2 201 73 -0.056 0.039 1000 -1000 -0.055 -1000
E-cadherin signaling in keratinocytes 0.0075 2 97 43 -0.045 0.047 1000 -1000 -0.052 -1000
p38 MAPK signaling pathway 0.0075 2 115 44 -0.038 0.046 1000 -1000 -0.048 -1000
Canonical NF-kappaB pathway 0.0037 1 75 39 -0.026 0.089 1000 -1000 -0.063 -1000
Circadian rhythm pathway 0.0037 1 28 22 -0.015 0.052 1000 -1000 -0.021 -1000
Insulin-mediated glucose transport 0.0037 1 48 32 -0.14 0.04 1000 -1000 -0.042 -1000
mTOR signaling pathway 0.0037 1 60 53 -0.006 0.04 1000 -1000 -0.053 -1000
ceramide signaling pathway 0.0037 1 77 49 -0.019 0.05 1000 -1000 -0.032 -1000
HIF-2-alpha transcription factor network 0.0037 1 55 43 -0.16 0.16 1000 -1000 -0.057 -1000
FoxO family signaling 0.0037 1 112 64 -0.068 0.096 1000 -1000 -0.053 -1000
Atypical NF-kappaB pathway 0.0037 1 34 31 0 0.053 1000 -1000 -0.022 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0037 1 160 125 -0.048 0.1 1000 -1000 -0.082 -1000
VEGFR1 specific signals 0.0037 1 60 56 -0.046 0.071 1000 -1000 -0.039 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 10 23 0.006 0.053 1000 -1000 -0.039 -1000
Arf6 downstream pathway 0.0000 0 13 43 -0.038 0.039 1000 -1000 -0.028 -1000
Signaling events mediated by HDAC Class I 0.0000 0 69 104 -0.03 0.064 1000 -1000 -0.056 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 16 27 0 0.037 1000 -1000 -0.041 -1000
Arf1 pathway 0.0000 0 4 54 0 0.038 1000 -1000 -0.031 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.045 1000 -1000 -0.023 -1000
Total NA 2259 132565 7203 -24 -990 131000 -131000 -6.6 -131000
FOXM1 transcription factor network

Figure S1.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S1.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 -0.63 0.5 -9999 0 -1 130 130
PLK1 -0.12 0.17 -9999 0 -10000 0 0
BIRC5 -0.24 0.18 -9999 0 -1.5 1 1
HSPA1B -0.63 0.5 -9999 0 -1.1 119 119
MAP2K1 -0.008 0.03 -9999 0 -10000 0 0
BRCA2 -0.64 0.5 -9999 0 -1.1 123 123
FOXM1 -0.81 0.68 -9999 0 -1.3 143 143
XRCC1 -0.63 0.5 -9999 0 -1 125 125
FOXM1B/p19 -0.73 0.49 -9999 0 -1.1 152 152
Cyclin D1/CDK4 -0.57 0.45 -9999 0 -0.96 124 124
CDC2 -0.67 0.53 -9999 0 -1.1 142 142
TGFA -0.55 0.44 -9999 0 -0.93 117 117
SKP2 -0.63 0.5 -9999 0 -1.1 122 122
CCNE1 -0.068 0.18 -9999 0 -0.49 41 41
CKS1B -0.63 0.5 -9999 0 -1.1 122 122
RB1 -0.24 0.14 -9999 0 -0.44 3 3
FOXM1C/SP1 -0.72 0.59 -9999 0 -1.2 141 141
AURKB -0.15 0.17 -9999 0 -10000 0 0
CENPF -0.71 0.53 -9999 0 -1.1 135 135
CDK4 0.005 0.012 -9999 0 -10000 0 0
MYC -0.56 0.45 -9999 0 -0.92 133 133
CHEK2 -0.008 0.03 -9999 0 -10000 0 0
ONECUT1 -0.61 0.48 -9999 0 -1 133 133
CDKN2A -0.22 0.25 -9999 0 -0.48 127 127
LAMA4 -0.64 0.5 -9999 0 -1.1 121 121
FOXM1B/HNF6 -0.72 0.58 -9999 0 -1.2 134 134
FOS -0.76 0.6 -9999 0 -1.2 146 146
SP1 0.015 0.001 -9999 0 -10000 0 0
CDC25B -0.63 0.5 -9999 0 -1 130 130
response to radiation -0.024 0.029 -9999 0 -10000 0 0
CENPB -0.63 0.5 -9999 0 -1.1 122 122
CENPA -0.71 0.53 -9999 0 -1.1 148 148
NEK2 -0.71 0.53 -9999 0 -1.1 142 142
HIST1H2BA -0.64 0.49 -9999 0 -1.1 125 125
CCNA2 -0.13 0.22 -9999 0 -0.5 72 72
EP300 0.015 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.75 0.6 -9999 0 -1.2 137 137
CCNB2 -0.71 0.54 -9999 0 -1.1 152 152
CCNB1 -0.69 0.55 -9999 0 -1.1 137 137
ETV5 -0.63 0.5 -9999 0 -1 130 130
ESR1 -0.72 0.56 -9999 0 -1.1 141 141
CCND1 -0.59 0.47 -9999 0 -0.98 125 125
GSK3A 0.001 0.025 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.12 0.18 -9999 0 -0.34 95 95
CDK2 0.009 0.007 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.03 0.034 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.72 0.48 -9999 0 -1.1 150 150
GAS1 -0.76 0.55 -9999 0 -1.1 155 155
MMP2 -0.66 0.53 -9999 0 -1.1 122 122
RB1/FOXM1C -0.62 0.5 -9999 0 -1 130 130
CREBBP 0.015 0 -9999 0 -10000 0 0
Glypican 2 network

Figure S2.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S2.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK -0.017 0.12 -9999 0 -0.48 17 17
GPC2 -0.14 0.23 -9999 0 -0.48 84 84
GPC2/Midkine -0.11 0.19 -9999 0 -0.36 93 93
neuron projection morphogenesis -0.11 0.19 -9999 0 -0.36 93 93
Aurora B signaling

Figure S3.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S3.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.14 0.14 -9999 0 -0.31 77 77
STMN1 -0.16 0.21 -9999 0 -0.37 129 129
Aurora B/RasGAP/Survivin -0.3 0.22 -9999 0 -0.52 118 118
Chromosomal passenger complex/Cul3 protein complex -0.16 0.16 -9999 0 -0.32 105 105
BIRC5 -0.36 0.22 -9999 0 -0.49 197 197
DES -0.5 0.36 -9999 0 -0.75 176 176
Aurora C/Aurora B/INCENP -0.1 0.14 -9999 0 -0.26 82 82
Aurora B/TACC1 -0.11 0.15 -9999 0 -0.28 120 120
Aurora B/PP2A -0.13 0.18 -9999 0 -0.33 120 120
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.018 0.041 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition -0.003 0.004 -9999 0 -10000 0 0
NDC80 -0.24 0.28 -9999 0 -0.48 140 140
Cul3 protein complex -0.057 0.17 -9999 0 -0.36 60 60
KIF2C -0.11 0.09 -9999 0 -0.19 125 125
PEBP1 0.006 0.006 -9999 0 -10000 0 0
KIF20A -0.36 0.22 -9999 0 -0.49 196 196
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.13 0.18 -9999 0 -0.33 120 120
SEPT1 0.011 0.043 -9999 0 -0.48 2 2
SMC2 0.013 0.03 -9999 0 -0.48 1 1
SMC4 0.015 0 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.049 0.06 -9999 0 -10000 0 0
PSMA3 0.015 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.002 0.003 -9999 0 -10000 0 0
H3F3B -0.062 0.092 -9999 0 -10000 0 0
AURKB -0.21 0.25 -9999 0 -0.49 120 120
AURKC 0 0.085 -9999 0 -0.48 8 8
CDCA8 -0.14 0.23 -9999 0 -0.5 78 78
cytokinesis -0.24 0.17 -9999 0 -0.39 129 129
Aurora B/Septin1 -0.22 0.17 -9999 0 -0.39 107 107
AURKA -0.15 0.23 -9999 0 -0.49 86 86
INCENP 0.005 0.032 -9999 0 -0.5 1 1
KLHL13 -0.098 0.23 -9999 0 -0.57 52 52
BUB1 -0.077 0.2 -9999 0 -0.49 49 49
hSgo1/Aurora B/Survivin -0.39 0.27 -9999 0 -0.59 158 158
EVI5 0.014 0.002 -9999 0 -10000 0 0
RhoA/GTP -0.25 0.2 -9999 0 -0.42 135 135
SGOL1 -0.21 0.25 -9999 0 -0.48 119 119
CENPA -0.16 0.13 -9999 0 -0.28 129 129
NCAPG -0.2 0.25 -9999 0 -0.48 118 118
Aurora B/HC8 Proteasome -0.13 0.18 -9999 0 -0.33 120 120
NCAPD2 0.013 0.03 -9999 0 -0.48 1 1
Aurora B/PP1-gamma -0.13 0.18 -9999 0 -0.33 120 120
RHOA 0.015 0 -9999 0 -10000 0 0
NCAPH -0.29 0.24 -9999 0 -0.48 163 163
NPM1 -0.058 0.074 -9999 0 -10000 0 0
RASA1 0.015 0 -9999 0 -10000 0 0
KLHL9 -0.011 0.12 -9999 0 -0.57 12 12
mitotic prometaphase -0.009 0.007 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.13 0.18 -9999 0 -0.33 120 120
PPP1CC 0.015 0 -9999 0 -10000 0 0
Centraspindlin -0.27 0.21 -9999 0 -0.46 141 141
RhoA/GDP 0.011 0 -9999 0 -10000 0 0
NSUN2 -0.058 0.074 -9999 0 -10000 0 0
MYLK -0.18 0.2 -9999 0 -0.43 89 89
KIF23 -0.24 0.25 -9999 0 -0.49 132 132
VIM -0.14 0.19 -9999 0 -0.34 121 121
RACGAP1 0.007 0.044 -9999 0 -0.49 2 2
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.058 0.074 -9999 0 -10000 0 0
Chromosomal passenger complex -0.19 0.15 -9999 0 -0.31 136 136
Chromosomal passenger complex/EVI5 -0.31 0.27 -9999 0 -0.54 134 134
TACC1 0.013 0.036 -9999 0 -0.57 1 1
PPP2R5D 0.015 0 -9999 0 -10000 0 0
CUL3 0.015 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

Figure S4.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S4.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.043 0.043 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.13 0.13 -9999 0 -0.39 18 18
JUN -0.096 0.14 -9999 0 -0.41 13 13
HRAS 0.015 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.15 0.18 -9999 0 -0.32 136 136
RAP1A 0.015 0 -9999 0 -10000 0 0
FRS2 0.006 0.068 -9999 0 -0.48 5 5
RAP1A/GDP 0.011 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.15 0.18 -9999 0 -0.32 136 136
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.015 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.015 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.15 0.17 -9999 0 -0.32 135 135
RHOA 0.015 0 -9999 0 -10000 0 0
RAP1A/GTP -0.15 0.14 -9999 0 -0.52 8 8
GRB7 -0.008 0.11 -9999 0 -0.5 12 12
RET51/GFRalpha1/GDNF -0.15 0.18 -9999 0 -0.32 136 136
MAPKKK cascade -0.14 0.13 -9999 0 -0.47 8 8
BCAR1 0.015 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.16 0.18 -9999 0 -0.33 136 136
lamellipodium assembly -0.13 0.13 -9999 0 -0.25 135 135
RET51/GFRalpha1/GDNF/SHC -0.15 0.18 -9999 0 -0.32 138 138
PIK3CA 0.015 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.15 0.17 -9999 0 -0.32 135 135
RET9/GFRalpha1/GDNF/Shank3 -0.15 0.17 -9999 0 -0.32 135 135
MAPK3 -0.11 0.16 -9999 0 -0.49 8 8
DOK1 0.013 0.03 -9999 0 -0.48 1 1
DOK6 -0.2 0.28 -9999 0 -0.57 99 99
PXN 0.015 0 -9999 0 -10000 0 0
neurite development -0.14 0.18 -9999 0 -0.37 70 70
DOK5 -0.037 0.16 -9999 0 -0.56 24 24
GFRA1 -0.28 0.29 -9999 0 -0.57 135 135
MAPK8 -0.1 0.14 -9999 0 -0.38 11 11
HRAS/GTP -0.16 0.16 -9999 0 -0.32 78 78
tube development -0.13 0.16 -9999 0 -0.29 135 135
MAPK1 -0.11 0.16 -9999 0 -0.49 8 8
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.11 0.14 -9999 0 -0.25 135 135
Rac1/GDP 0.011 0 -9999 0 -10000 0 0
SRC 0.015 0 -9999 0 -10000 0 0
PDLIM7 0.015 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.25 0.25 -9999 0 -0.46 122 122
SHC1 0.013 0.03 -9999 0 -0.48 1 1
RET51/GFRalpha1/GDNF/Dok4 -0.15 0.18 -9999 0 -0.32 136 136
RET51/GFRalpha1/GDNF/Dok5 -0.18 0.22 -9999 0 -0.36 141 141
PRKCA 0.013 0.036 -9999 0 -0.57 1 1
HRAS/GDP 0.011 0 -9999 0 -10000 0 0
CREB1 -0.13 0.17 -9999 0 -0.29 135 135
PIK3R1 0.015 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.11 0.14 -9999 0 -0.25 135 135
RET51/GFRalpha1/GDNF/Grb7 -0.16 0.19 -9999 0 -0.33 137 137
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.007 0.11 -9999 0 -0.52 11 11
DOK4 0.015 0 -9999 0 -10000 0 0
JNK cascade -0.094 0.14 -9999 0 -0.4 13 13
RET9/GFRalpha1/GDNF/FRS2 -0.15 0.17 -9999 0 -0.32 139 139
SHANK3 0.015 0 -9999 0 -10000 0 0
RASA1 0.015 0 -9999 0 -10000 0 0
NCK1 0.015 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.11 0.14 -9999 0 -0.25 135 135
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.12 0.15 -9999 0 -0.25 137 137
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.11 0.15 -9999 0 -0.25 136 136
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.12 0.16 -9999 0 -0.26 136 136
PI3K -0.16 0.22 -9999 0 -0.37 135 135
SOS1 0.015 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.13 0.16 -9999 0 -0.29 135 135
GRB10 0.013 0.036 -9999 0 -0.57 1 1
activation of MAPKK activity -0.11 0.14 -9999 0 -0.39 9 9
RET51/GFRalpha1/GDNF/FRS2 -0.16 0.18 -9999 0 -0.32 140 140
GAB1 0.015 0 -9999 0 -10000 0 0
IRS1 0.002 0.086 -9999 0 -0.57 6 6
IRS2 -0.004 0.1 -9999 0 -0.57 9 9
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.12 0.16 -9999 0 -0.26 136 136
RET51/GFRalpha1/GDNF/PKC alpha -0.15 0.18 -9999 0 -0.32 136 136
GRB2 0.015 0 -9999 0 -10000 0 0
PRKACA 0.015 0 -9999 0 -10000 0 0
GDNF 0.002 0.052 -9999 0 -0.48 3 3
RAC1 0.015 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.16 0.19 -9999 0 -0.33 139 139
Rac1/GTP -0.16 0.15 -9999 0 -0.3 135 135
RET9/GFRalpha1/GDNF -0.17 0.19 -9999 0 -0.36 135 135
GFRalpha1/GDNF -0.2 0.22 -9999 0 -0.42 135 135
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

Figure S5.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S5.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FOXP3 0.003 0.098 -10000 0 -0.62 6 6
NFATC2 -0.11 0.28 -10000 0 -0.63 49 49
NFATC3 -0.087 0.13 -10000 0 -0.31 25 25
CD40LG -0.53 0.56 -10000 0 -1.1 118 118
ITCH 0.025 0.086 -10000 0 -0.38 1 1
CBLB 0.026 0.083 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.38 0.45 -10000 0 -1.1 61 61
JUNB 0.009 0.061 -10000 0 -0.57 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.028 0.084 -10000 0 -0.28 26 26
T cell anergy -0.012 0.13 -10000 0 -0.38 26 26
TLE4 -0.067 0.24 -10000 0 -0.58 39 39
Jun/NFAT1-c-4/p21SNFT -0.44 0.56 -10000 0 -1 107 107
AP-1/NFAT1-c-4 -0.62 0.7 -10000 0 -1.3 118 118
IKZF1 -0.064 0.24 -10000 0 -0.58 35 35
T-helper 2 cell differentiation -0.23 0.36 -10000 0 -0.89 46 46
AP-1/NFAT1 -0.19 0.26 -10000 0 -0.5 89 89
CALM1 0.013 0.054 -10000 0 -10000 0 0
EGR2 -0.49 0.74 -10000 0 -1.6 69 69
EGR3 -0.69 0.84 -10000 0 -1.6 122 122
NFAT1/FOXP3 -0.079 0.22 -10000 0 -0.51 43 43
EGR1 -0.12 0.24 -10000 0 -0.57 62 62
JUN -0.006 0.095 -10000 0 -0.57 7 7
EGR4 -0.015 0.12 -10000 0 -0.54 14 14
mol:Ca2+ -0.002 0.058 -10000 0 -10000 0 0
GBP3 -0.059 0.22 -10000 0 -0.52 37 37
FOSL1 -0.026 0.15 -10000 0 -0.57 19 19
NFAT1-c-4/MAF/IRF4 -0.43 0.57 -10000 0 -1 111 111
DGKA -0.052 0.21 -10000 0 -0.5 34 34
CREM 0.015 0.001 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.46 0.55 -10000 0 -1 118 118
CTLA4 -0.066 0.23 -10000 0 -0.6 30 30
NFAT1-c-4 (dimer)/EGR1 -0.49 0.63 -10000 0 -1.1 117 117
NFAT1-c-4 (dimer)/EGR4 -0.44 0.57 -10000 0 -1 119 119
FOS -0.17 0.27 -10000 0 -0.58 80 80
IFNG -0.23 0.3 -10000 0 -0.81 39 39
T cell activation -0.24 0.32 -10000 0 -0.72 53 53
MAF -0.002 0.099 -10000 0 -0.57 8 8
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.35 0.5 0.91 89 -10000 0 89
TNF -0.42 0.53 -10000 0 -0.96 113 113
FASLG -0.67 0.82 -10000 0 -1.4 129 129
TBX21 -0.013 0.12 -10000 0 -0.56 11 11
BATF3 0.007 0.068 -10000 0 -0.55 4 4
PRKCQ -0.045 0.18 -10000 0 -0.56 28 28
PTPN1 -0.052 0.21 -10000 0 -0.5 34 34
NFAT1-c-4/ICER1 -0.45 0.55 -10000 0 -0.98 121 121
GATA3 -0.028 0.15 -10000 0 -0.56 20 20
T-helper 1 cell differentiation -0.21 0.31 -10000 0 -0.76 44 44
IL2RA -0.37 0.43 -10000 0 -0.92 77 77
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.052 0.21 -10000 0 -0.56 24 24
E2F1 -0.093 0.21 -10000 0 -0.47 62 62
PPARG -0.034 0.16 -10000 0 -0.56 23 23
SLC3A2 -0.052 0.21 -10000 0 -0.5 34 34
IRF4 -0.034 0.16 -10000 0 -0.56 23 23
PTGS2 -0.56 0.57 -10000 0 -1.1 121 121
CSF2 -0.54 0.53 -10000 0 -1 122 122
JunB/Fra1/NFAT1-c-4 -0.43 0.56 -10000 0 -1 115 115
IL4 -0.25 0.38 -10000 0 -0.96 45 45
IL5 -0.51 0.53 -10000 0 -1 116 116
IL2 -0.24 0.32 -10000 0 -0.76 48 48
IL3 -0.08 0.063 -10000 0 -10000 0 0
RNF128 -0.016 0.2 -10000 0 -0.63 27 27
NFATC1 -0.35 0.51 -10000 0 -0.92 88 88
CDK4 0.18 0.27 0.57 55 -10000 0 55
PTPRK -0.052 0.21 -10000 0 -0.53 28 28
IL8 -0.54 0.56 -10000 0 -1.1 121 121
POU2F1 0.015 0.002 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

Figure S6.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S6.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTGS2 -0.24 0.5 -9999 0 -1.1 62 62
MKNK1 0.015 0 -9999 0 -10000 0 0
MAPK14 -0.056 0.14 -9999 0 -0.3 67 67
ATF2/c-Jun -0.039 0.18 -9999 0 -0.85 8 8
MAPK11 -0.056 0.14 -9999 0 -0.39 12 12
MITF -0.089 0.23 -9999 0 -0.4 79 79
MAPKAPK5 -0.057 0.18 -9999 0 -0.35 67 67
KRT8 -0.069 0.21 -9999 0 -0.39 69 69
MAPKAPK3 0.015 0 -9999 0 -10000 0 0
MAPKAPK2 0.015 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.085 0.22 -9999 0 -0.44 67 67
CEBPB -0.058 0.18 -9999 0 -0.36 67 67
SLC9A1 -0.057 0.18 -9999 0 -0.35 67 67
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.052 0.18 -9999 0 -0.35 67 67
p38alpha-beta/MNK1 -0.054 0.18 -9999 0 -0.47 14 14
JUN -0.039 0.18 -9999 0 -0.84 8 8
PPARGC1A -0.21 0.27 -9999 0 -0.42 149 149
USF1 -0.057 0.18 -9999 0 -0.35 67 67
RAB5/GDP/GDI1 -0.066 0.11 -9999 0 -0.35 12 12
NOS2 -0.091 0.25 -9999 0 -0.9 13 13
DDIT3 -0.057 0.18 -9999 0 -0.35 67 67
RAB5A 0.015 0 -9999 0 -10000 0 0
HSPB1 -0.038 0.15 -9999 0 -0.41 12 12
p38alpha-beta/HBP1 -0.054 0.18 -9999 0 -0.34 67 67
CREB1 -0.062 0.19 -9999 0 -0.37 67 67
RAB5/GDP 0.011 0 -9999 0 -10000 0 0
EIF4E -0.041 0.15 -9999 0 -0.43 12 12
RPS6KA4 -0.057 0.18 -9999 0 -0.35 67 67
PLA2G4A -0.062 0.19 -9999 0 -0.54 19 19
GDI1 -0.057 0.18 -9999 0 -0.35 67 67
TP53 -0.076 0.22 -9999 0 -0.43 67 67
RPS6KA5 -0.067 0.2 -9999 0 -0.36 72 72
ESR1 -0.13 0.25 -9999 0 -0.42 99 99
HBP1 0.015 0 -9999 0 -10000 0 0
MEF2C -0.066 0.19 -9999 0 -0.37 70 70
MEF2A -0.057 0.18 -9999 0 -0.35 67 67
EIF4EBP1 -0.063 0.19 -9999 0 -0.38 67 67
KRT19 -0.076 0.21 -9999 0 -0.39 73 73
ELK4 -0.057 0.18 -9999 0 -0.35 67 67
ATF6 -0.057 0.18 -9999 0 -0.35 67 67
ATF1 -0.062 0.19 -9999 0 -0.37 67 67
p38alpha-beta/MAPKAPK2 -0.054 0.18 -9999 0 -0.47 14 14
p38alpha-beta/MAPKAPK3 -0.054 0.18 -9999 0 -0.34 67 67
Signaling events mediated by the Hedgehog family

Figure S7.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S7.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB2 -0.062 0.24 -10000 0 -0.63 33 33
IHH -0.063 0.18 -10000 0 -0.5 38 38
SHH Np/Cholesterol/GAS1 -0.17 0.2 -10000 0 -0.34 141 141
LRPAP1 0.013 0.03 -10000 0 -0.48 1 1
dorsoventral neural tube patterning 0.17 0.2 0.34 141 -10000 0 141
SMO/beta Arrestin2 -0.046 0.17 -10000 0 -0.5 19 19
SMO -0.057 0.18 -10000 0 -0.5 25 25
AKT1 -0.002 0.081 -10000 0 -0.3 1 1
ARRB2 0.015 0 -10000 0 -10000 0 0
BOC -0.033 0.16 -10000 0 -0.57 22 22
ADRBK1 0.015 0 -10000 0 -10000 0 0
heart looping -0.056 0.17 -10000 0 -0.49 25 25
STIL -0.15 0.21 -10000 0 -0.46 59 59
DHH N/PTCH2 -0.015 0.12 -10000 0 -0.41 23 23
DHH N/PTCH1 -0.035 0.15 -10000 0 -0.46 17 17
PIK3CA 0.015 0 -10000 0 -10000 0 0
DHH -0.008 0.11 -10000 0 -0.57 10 10
PTHLH -0.11 0.37 -10000 0 -1 33 33
determination of left/right symmetry -0.056 0.17 -10000 0 -0.49 25 25
PIK3R1 0.015 0 -10000 0 -10000 0 0
skeletal system development -0.11 0.36 -10000 0 -1 33 33
IHH N/Hhip -0.14 0.23 -10000 0 -0.44 95 95
DHH N/Hhip -0.1 0.2 -10000 0 -0.41 77 77
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.056 0.17 -10000 0 -0.49 25 25
pancreas development -0.14 0.25 -10000 0 -0.56 69 69
HHAT 0.015 0 -10000 0 -10000 0 0
PI3K 0.022 0 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.12 0.24 -10000 0 -0.56 62 62
somite specification -0.056 0.17 -10000 0 -0.49 25 25
SHH Np/Cholesterol/PTCH1 -0.12 0.19 -10000 0 -0.44 45 45
SHH Np/Cholesterol/PTCH2 -0.11 0.17 -10000 0 -0.32 105 105
SHH Np/Cholesterol/Megalin -0.15 0.2 -10000 0 -0.34 125 125
SHH -0.14 0.2 -10000 0 -0.41 97 97
catabolic process -0.034 0.16 -10000 0 -0.52 13 13
SMO/Vitamin D3 -0.11 0.2 -10000 0 -0.47 39 39
SHH Np/Cholesterol/Hhip -0.18 0.21 -10000 0 -0.37 138 138
LRP2 -0.083 0.2 -10000 0 -0.48 52 52
receptor-mediated endocytosis -0.15 0.21 -10000 0 -0.47 50 50
SHH Np/Cholesterol/BOC -0.12 0.18 -10000 0 -0.33 109 109
SHH Np/Cholesterol/CDO -0.14 0.19 -10000 0 -0.33 127 127
mesenchymal cell differentiation 0.18 0.21 0.37 138 -10000 0 138
mol:Vitamin D3 -0.12 0.19 -10000 0 -0.44 45 45
IHH N/PTCH2 -0.046 0.14 -10000 0 -0.4 29 29
CDON -0.072 0.21 -10000 0 -0.57 40 40
IHH N/PTCH1 -0.034 0.16 -10000 0 -0.53 13 13
Megalin/LRPAP1 -0.05 0.14 -10000 0 -0.34 53 53
PTCH2 -0.013 0.12 -10000 0 -0.57 13 13
SHH Np/Cholesterol -0.11 0.15 -10000 0 -0.32 97 97
PTCH1 -0.034 0.16 -10000 0 -0.52 13 13
HHIP -0.14 0.25 -10000 0 -0.56 69 69
Nongenotropic Androgen signaling

Figure S8.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S8.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.013 0.001 -10000 0 -10000 0 0
GNB1/GNG2 -0.09 0.16 -10000 0 -0.31 92 92
regulation of S phase of mitotic cell cycle -0.062 0.13 -10000 0 -0.25 90 90
GNAO1 -0.16 0.27 -10000 0 -0.57 80 80
HRAS 0.014 0.002 -10000 0 -10000 0 0
SHBG/T-DHT 0.01 0.002 -10000 0 -10000 0 0
PELP1 0.014 0.002 -10000 0 -10000 0 0
AKT1 0.013 0.001 -10000 0 -10000 0 0
MAP2K1 -0.078 0.15 -10000 0 -0.35 35 35
T-DHT/AR -0.14 0.2 -10000 0 -0.42 90 90
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.003 -10000 0 -0.006 80 80
GNAI2 0.015 0 -10000 0 -10000 0 0
GNAI3 0.015 0 -10000 0 -10000 0 0
GNAI1 0.013 0.035 -10000 0 -0.57 1 1
mol:GDP -0.15 0.21 -10000 0 -0.44 90 90
cell proliferation -0.15 0.23 -10000 0 -0.45 81 81
PIK3CA 0.015 0 -10000 0 -10000 0 0
FOS -0.24 0.39 -10000 0 -0.84 80 80
mol:Ca2+ -0.044 0.044 -10000 0 -0.086 120 120
MAPK3 -0.12 0.19 -10000 0 -0.48 35 35
MAPK1 -0.065 0.12 -10000 0 -0.27 34 34
PIK3R1 0.015 0 -10000 0 -10000 0 0
mol:IP3 -0.001 0.002 -10000 0 -0.004 80 80
cAMP biosynthetic process 0.037 0.037 -10000 0 -10000 0 0
GNG2 0.009 0.061 -10000 0 -0.57 3 3
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 80 80
HRAS/GTP -0.1 0.13 -10000 0 -0.29 90 90
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0.014 0.002 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 80 80
PI3K 0.021 0 -10000 0 -10000 0 0
apoptosis 0.13 0.22 0.45 80 -10000 0 80
T-DHT/AR/PELP1 -0.11 0.17 -10000 0 -0.35 90 90
HRAS/GDP -0.14 0.2 -10000 0 -0.41 90 90
CREB1 -0.14 0.24 -10000 0 -0.48 80 80
RAC1-CDC42/GTP 0 0 -10000 0 -10000 0 0
AR -0.18 0.28 -10000 0 -0.57 90 90
GNB1 0.015 0 -10000 0 -10000 0 0
RAF1 -0.08 0.15 -10000 0 -0.34 35 35
RAC1-CDC42/GDP -0.13 0.19 -10000 0 -0.39 90 90
T-DHT/AR/PELP1/Src -0.09 0.16 -10000 0 -0.31 90 90
MAP2K2 -0.078 0.15 -10000 0 -0.35 35 35
T-DHT/AR/PELP1/Src/PI3K -0.062 0.13 -10000 0 -0.25 90 90
GNAZ -0.12 0.24 -10000 0 -0.57 60 60
SHBG 0.015 0.003 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.15 0.25 -10000 0 -0.47 90 90
mol:T-DHT 0 0.001 -10000 0 -0.003 46 46
RAC1 0.015 0 -10000 0 -10000 0 0
GNRH1 0.013 0.001 -10000 0 -10000 0 0
Gi family/GTP -0.16 0.21 -10000 0 -0.42 85 85
CDC42 0.015 0 -10000 0 -10000 0 0
IL4-mediated signaling events

Figure S9.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S9.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.48 0.55 -10000 0 -1.2 77 77
STAT6 (cleaved dimer) -0.55 0.55 -10000 0 -1.1 101 101
IGHG1 -0.15 0.2 -10000 0 -0.38 47 47
IGHG3 -0.47 0.53 -10000 0 -1.1 87 87
AKT1 -0.21 0.31 -10000 0 -0.73 41 41
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.17 0.3 -10000 0 -0.76 29 29
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.23 0.33 -10000 0 -0.68 53 53
THY1 -0.48 0.55 -10000 0 -1.2 77 77
MYB -0.047 0.16 -10000 0 -0.49 33 33
HMGA1 0.011 0.043 -10000 0 -0.48 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.3 0.4 -10000 0 -0.78 77 77
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.23 0.33 -10000 0 -0.69 50 50
SP1 0.023 0.005 -10000 0 -10000 0 0
INPP5D 0.002 0.086 -10000 0 -0.57 6 6
SOCS5 0.029 0.017 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.5 0.56 -10000 0 -1.2 85 85
SOCS1 -0.29 0.35 -10000 0 -0.75 66 66
SOCS3 -0.3 0.46 -10000 0 -1.3 38 38
FCER2 -0.72 0.73 -10000 0 -1.4 124 124
PARP14 0.01 0.014 -10000 0 -10000 0 0
CCL17 -0.5 0.55 -10000 0 -1.2 83 83
GRB2 0.015 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.17 0.25 -10000 0 -0.64 27 27
T cell proliferation -0.48 0.58 -10000 0 -1.2 82 82
IL4R/JAK1 -0.48 0.56 -10000 0 -1.2 80 80
EGR2 -0.66 0.72 -10000 0 -1.4 102 102
JAK2 -0.008 0.049 -10000 0 -0.6 1 1
JAK3 0.013 0.045 -10000 0 -0.49 2 2
PIK3R1 0.015 0 -10000 0 -10000 0 0
JAK1 0.008 0.016 -10000 0 -10000 0 0
COL1A2 -0.18 0.34 -10000 0 -1.6 12 12
CCL26 -0.49 0.57 -10000 0 -1.2 79 79
IL4R -0.51 0.6 -10000 0 -1.3 79 79
PTPN6 0.026 0.013 -10000 0 -10000 0 0
IL13RA2 -0.5 0.58 -10000 0 -1.2 81 81
IL13RA1 -0.005 0.032 -10000 0 -10000 0 0
IRF4 -0.25 0.5 -10000 0 -1.3 41 41
ARG1 -0.12 0.2 -10000 0 -0.86 6 6
CBL -0.28 0.37 -10000 0 -0.76 69 69
GTF3A 0.024 0.004 -10000 0 -10000 0 0
PIK3CA 0.015 0 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.01 0.055 -10000 0 -0.44 1 1
IRF4/BCL6 -0.2 0.45 -10000 0 -1.2 39 39
CD40LG -0.054 0.19 -10000 0 -0.57 31 31
MAPK14 -0.3 0.42 -10000 0 -0.86 64 64
mitosis -0.2 0.3 -10000 0 -0.68 41 41
STAT6 -0.57 0.69 -10000 0 -1.4 87 87
SPI1 0 0.095 -10000 0 -0.54 8 8
RPS6KB1 -0.19 0.28 -10000 0 -0.68 35 35
STAT6 (dimer) -0.57 0.69 -10000 0 -1.4 87 87
STAT6 (dimer)/PARP14 -0.55 0.62 -10000 0 -1.2 102 102
mast cell activation 0.011 0.014 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.22 0.34 -10000 0 -0.76 43 43
FRAP1 -0.21 0.31 -10000 0 -0.73 41 41
LTA -0.5 0.58 -10000 0 -1.2 79 79
FES 0.013 0.036 -10000 0 -0.57 1 1
T-helper 1 cell differentiation 0.55 0.64 1.3 87 -10000 0 87
CCL11 -0.5 0.59 -10000 0 -1.3 80 80
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.22 0.33 -10000 0 -0.74 42 42
IL2RG -0.01 0.12 -10000 0 -0.53 13 13
IL10 -0.51 0.6 -10000 0 -1.3 80 80
IRS1 0.002 0.086 -10000 0 -0.57 6 6
IRS2 -0.004 0.1 -10000 0 -0.57 9 9
IL4 -0.1 0.13 -10000 0 -10000 0 0
IL5 -0.48 0.55 -10000 0 -1.2 77 77
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.37 0.41 -10000 0 -0.87 79 79
COL1A1 -0.15 0.26 -10000 0 -1.7 4 4
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.49 0.57 -10000 0 -1.2 77 77
IL2R gamma/JAK3 -0.003 0.1 -10000 0 -0.43 13 13
TFF3 -0.64 0.69 -10000 0 -1.4 106 106
ALOX15 -0.52 0.56 -10000 0 -1.2 83 83
MYBL1 0.009 0.053 -10000 0 -0.48 3 3
T-helper 2 cell differentiation -0.41 0.46 -10000 0 -0.96 84 84
SHC1 0.013 0.03 -10000 0 -0.48 1 1
CEBPB 0.014 0.038 -10000 0 -0.57 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.22 0.32 -10000 0 -0.66 53 53
mol:PI-3-4-5-P3 -0.21 0.31 -10000 0 -0.73 41 41
PI3K -0.23 0.34 -10000 0 -0.79 41 41
DOK2 -0.006 0.11 -10000 0 -0.56 10 10
ETS1 0.026 0.014 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.16 0.24 -10000 0 -0.61 26 26
ITGB3 -0.53 0.64 -10000 0 -1.3 83 83
PIGR -0.79 0.72 -10000 0 -1.4 134 134
IGHE 0.034 0.048 -10000 0 -0.22 1 1
MAPKKK cascade -0.16 0.24 -10000 0 -0.6 25 25
BCL6 0.02 0.01 -10000 0 -10000 0 0
OPRM1 -0.48 0.55 -10000 0 -1.2 79 79
RETNLB -0.49 0.55 -10000 0 -1.2 78 78
SELP -0.61 0.7 -10000 0 -1.4 94 94
AICDA -0.47 0.53 -10000 0 -1.2 78 78
Endothelins

Figure S10.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S10.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.002 0.2 -10000 0 -0.5 25 25
PTK2B 0.013 0.036 -10000 0 -0.57 1 1
mol:Ca2+ -0.007 0.21 -10000 0 -0.64 16 16
EDN1 0.037 0.12 -10000 0 -0.42 9 9
EDN3 -0.004 0.067 -10000 0 -0.48 5 5
EDN2 -0.05 0.18 -10000 0 -0.52 32 32
HRAS/GDP -0.069 0.24 -10000 0 -0.51 45 45
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.027 0.18 -10000 0 -0.42 33 33
ADCY4 -0.13 0.24 -10000 0 -0.55 44 44
ADCY5 -0.28 0.32 -10000 0 -0.62 105 105
ADCY6 -0.13 0.24 -10000 0 -0.57 41 41
ADCY7 -0.13 0.24 -10000 0 -0.57 40 40
ADCY1 -0.14 0.25 -10000 0 -0.58 44 44
ADCY2 -0.24 0.31 -10000 0 -0.64 80 80
ADCY3 -0.13 0.24 -10000 0 -0.57 41 41
ADCY8 -0.14 0.24 -10000 0 -0.57 42 42
ADCY9 -0.14 0.25 -10000 0 -0.58 42 42
arachidonic acid secretion -0.12 0.28 -10000 0 -0.5 74 74
ETB receptor/Endothelin-1/Gq/GTP -0.046 0.19 -10000 0 -0.45 37 37
GNAO1 -0.16 0.27 -10000 0 -0.57 80 80
HRAS 0.012 0.006 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.052 0.23 0.24 124 -0.48 22 146
ETA receptor/Endothelin-1/Gs/GTP -0.1 0.3 0.23 69 -0.58 44 113
mol:GTP 0 0.005 -10000 0 -10000 0 0
COL3A1 -0.003 0.22 -10000 0 -0.58 22 22
EDNRB -0.049 0.18 -10000 0 -0.56 30 30
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.003 0.21 -10000 0 -0.49 27 27
CYSLTR1 -0.022 0.26 -10000 0 -0.62 33 33
SLC9A1 0.003 0.11 -10000 0 -0.3 15 15
mol:GDP -0.082 0.25 -10000 0 -0.51 52 52
SLC9A3 -0.025 0.23 -10000 0 -0.61 28 28
RAF1 -0.13 0.28 -10000 0 -0.53 66 66
JUN -0.023 0.26 -10000 0 -0.84 18 18
JAK2 0.001 0.21 -10000 0 -0.47 30 30
mol:IP3 -0.051 0.21 -10000 0 -0.5 36 36
ETA receptor/Endothelin-1 0.042 0.28 0.27 124 -0.5 37 161
PLCB1 -0.005 0.099 -10000 0 -0.57 8 8
PLCB2 0.01 0.036 -10000 0 -0.57 1 1
ETA receptor/Endothelin-3 -0.028 0.18 -10000 0 -0.44 38 38
FOS -0.27 0.48 -10000 0 -0.94 85 85
Gai/GDP -0.24 0.4 -10000 0 -0.84 80 80
CRK 0.015 0.001 -10000 0 -10000 0 0
mol:Ca ++ -0.067 0.26 -10000 0 -0.55 48 48
BCAR1 0.016 0.001 -10000 0 -10000 0 0
PRKCB1 -0.052 0.2 -10000 0 -0.49 36 36
GNAQ 0.014 0.008 -10000 0 -10000 0 0
GNAZ -0.12 0.24 -10000 0 -0.57 60 60
GNAL -0.23 0.29 -10000 0 -0.57 112 112
Gs family/GDP -0.21 0.25 -10000 0 -0.52 91 91
ETA receptor/Endothelin-1/Gq/GTP -0.028 0.2 -10000 0 -0.47 32 32
MAPK14 -0.03 0.17 -10000 0 -0.48 25 25
TRPC6 -0.01 0.22 -10000 0 -0.68 16 16
GNAI2 0.015 0 -10000 0 -10000 0 0
GNAI3 0.015 0 -10000 0 -10000 0 0
GNAI1 0.013 0.036 -10000 0 -0.57 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.039 0.18 -10000 0 -0.47 29 29
ETB receptor/Endothelin-2 -0.07 0.19 -10000 0 -0.42 56 56
ETB receptor/Endothelin-3 -0.039 0.14 -10000 0 -0.4 35 35
ETB receptor/Endothelin-1 -0.01 0.17 -10000 0 -0.39 39 39
MAPK3 -0.23 0.42 -10000 0 -0.79 87 87
MAPK1 -0.23 0.42 -10000 0 -0.79 87 87
Rac1/GDP -0.068 0.24 -10000 0 -0.5 46 46
cAMP biosynthetic process -0.22 0.28 -10000 0 -0.52 110 110
MAPK8 -0.026 0.25 -10000 0 -0.71 21 21
SRC 0.015 0 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.11 0.21 -10000 0 -0.42 66 66
p130Cas/CRK/Src/PYK2 -0.059 0.24 -10000 0 -0.54 38 38
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.068 0.24 -10000 0 -0.5 45 45
COL1A2 -0.038 0.3 -10000 0 -0.87 23 23
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.066 0.2 -10000 0 -0.41 65 65
mol:DAG -0.051 0.21 -10000 0 -0.5 36 36
MAP2K2 -0.17 0.33 -10000 0 -0.58 93 93
MAP2K1 -0.17 0.33 -10000 0 -0.58 93 93
EDNRA -0.022 0.24 -10000 0 -0.6 34 34
positive regulation of muscle contraction 0.01 0.18 -10000 0 -0.46 21 21
Gq family/GDP -0.13 0.21 -10000 0 -0.51 51 51
HRAS/GTP -0.099 0.24 -10000 0 -0.51 53 53
PRKCH -0.044 0.2 -10000 0 -0.5 34 34
RAC1 0.015 0 -10000 0 -10000 0 0
PRKCA -0.045 0.2 -10000 0 -0.5 34 34
PRKCB -0.13 0.26 -10000 0 -0.49 75 75
PRKCE -0.043 0.2 -10000 0 -0.49 34 34
PRKCD -0.045 0.2 -10000 0 -0.48 36 36
PRKCG -0.055 0.21 -10000 0 -0.49 37 37
regulation of vascular smooth muscle contraction -0.32 0.55 -10000 0 -1.1 85 85
PRKCQ -0.075 0.23 -10000 0 -0.5 49 49
PLA2G4A -0.14 0.31 -10000 0 -0.55 74 74
GNA14 -0.08 0.21 -10000 0 -0.57 43 43
GNA15 0.01 0.05 -10000 0 -0.57 2 2
GNA12 0.015 0 -10000 0 -10000 0 0
GNA11 0.013 0.036 -10000 0 -0.57 1 1
Rac1/GTP 0.053 0.23 0.24 124 -0.47 24 148
MMP1 -0.18 0.21 0.32 2 -0.37 135 137
Signaling events mediated by Stem cell factor receptor (c-Kit)

Figure S11.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S11.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K1 -0.064 0.2 -10000 0 -0.4 64 64
CRKL -0.069 0.2 -10000 0 -0.42 63 63
HRAS -0.069 0.22 -10000 0 -0.4 70 70
mol:PIP3 -0.078 0.19 -10000 0 -0.4 64 64
SPRED1 0.015 0 -10000 0 -10000 0 0
SPRED2 0.015 0 -10000 0 -10000 0 0
GAB1 -0.079 0.21 -10000 0 -0.44 64 64
FOXO3 -0.055 0.18 -10000 0 -0.38 63 63
AKT1 -0.068 0.2 -10000 0 -0.41 63 63
BAD -0.055 0.18 -10000 0 -0.38 63 63
megakaryocyte differentiation -0.084 0.21 -10000 0 -0.43 69 69
GSK3B -0.055 0.18 -10000 0 -0.38 63 63
RAF1 -0.045 0.18 -10000 0 -0.38 32 32
SHC1 0.013 0.03 -10000 0 -0.48 1 1
STAT3 -0.079 0.21 -10000 0 -0.44 64 64
STAT1 -0.21 0.48 -10000 0 -1 68 68
HRAS/SPRED1 -0.046 0.18 -10000 0 -0.38 32 32
cell proliferation -0.08 0.21 -10000 0 -0.44 64 64
PIK3CA 0.015 0.001 -10000 0 -10000 0 0
TEC 0.015 0 -10000 0 -10000 0 0
RPS6KB1 -0.078 0.21 -10000 0 -0.43 66 66
HRAS/SPRED2 -0.046 0.18 -10000 0 -0.38 32 32
LYN/TEC/p62DOK -0.1 0.18 -10000 0 -0.41 63 63
MAPK3 -0.017 0.13 -10000 0 -0.28 26 26
STAP1 -0.098 0.22 -10000 0 -0.44 72 72
GRAP2 -0.059 0.19 -10000 0 -0.57 34 34
JAK2 -0.21 0.38 -10000 0 -0.85 68 68
STAT1 (dimer) -0.21 0.47 -10000 0 -1 68 68
mol:Gleevec 0.002 0.008 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.11 0.19 -10000 0 -0.43 65 65
actin filament polymerization -0.08 0.21 -10000 0 -0.43 65 65
LYN 0.015 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.12 0.3 -10000 0 -0.62 66 66
PIK3R1 0.015 0.001 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.048 0.19 -10000 0 -0.37 63 63
PI3K -0.061 0.2 -10000 0 -0.41 63 63
PTEN 0.015 0 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.27 0.58 -10000 0 -1.3 65 65
MAPK8 -0.083 0.22 -10000 0 -0.45 64 64
STAT3 (dimer) -0.077 0.2 -10000 0 -0.43 64 64
positive regulation of transcription -0.009 0.11 -10000 0 -0.24 21 21
mol:GDP -0.11 0.2 -10000 0 -0.42 70 70
PIK3C2B -0.079 0.21 -10000 0 -0.44 64 64
CBL/CRKL -0.057 0.19 -10000 0 -0.39 63 63
FER -0.08 0.21 -10000 0 -0.44 64 64
SH2B3 -0.079 0.21 -10000 0 -0.44 64 64
PDPK1 -0.064 0.17 -10000 0 -0.37 63 63
SNAI2 -0.083 0.21 -10000 0 -0.45 65 65
positive regulation of cell proliferation -0.14 0.35 -10000 0 -0.73 68 68
KITLG 0.007 0.074 -10000 0 -0.59 4 4
cell motility -0.14 0.35 -10000 0 -0.73 68 68
PTPN6 0.018 0.011 -10000 0 -10000 0 0
EPOR -0.03 0.15 -10000 0 -0.54 2 2
STAT5A (dimer) -0.11 0.29 -10000 0 -0.6 68 68
SOCS1 0.013 0.03 -10000 0 -0.48 1 1
cell migration 0.1 0.22 0.44 76 -10000 0 76
SOS1 0.015 0 -10000 0 -10000 0 0
EPO -0.034 0.14 -10000 0 -0.48 24 24
VAV1 -0.015 0.13 -10000 0 -0.56 14 14
GRB10 -0.081 0.21 -10000 0 -0.44 64 64
PTPN11 0.017 0.008 -10000 0 -10000 0 0
SCF/KIT -0.092 0.22 -10000 0 -0.45 70 70
GO:0007205 0.003 0.011 -10000 0 -10000 0 0
MAP2K1 -0.024 0.14 -10000 0 -0.31 26 26
CBL 0.015 0 -10000 0 -10000 0 0
KIT -0.28 0.6 -10000 0 -1.4 63 63
MAP2K2 -0.024 0.14 -10000 0 -0.31 26 26
SHC/Grb2/SOS1 -0.1 0.18 -10000 0 -0.41 63 63
STAT5A -0.12 0.3 -10000 0 -0.62 68 68
GRB2 0.015 0 -10000 0 -10000 0 0
response to radiation -0.08 0.21 -10000 0 -0.44 65 65
SHC/GRAP2 -0.033 0.14 -10000 0 -0.4 35 35
PTPRO -0.087 0.21 -10000 0 -0.44 69 69
SH2B2 -0.082 0.21 -10000 0 -0.44 65 65
DOK1 0.013 0.03 -10000 0 -0.48 1 1
MATK -0.1 0.23 -10000 0 -0.45 76 76
CREBBP 0.032 0.02 -10000 0 -10000 0 0
BCL2 -0.073 0.33 -10000 0 -1.5 12 12
IGF1 pathway

Figure S12.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S12.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.015 0 -10000 0 -10000 0 0
PTK2 0.015 0 -10000 0 -10000 0 0
CRKL -0.12 0.16 -10000 0 -0.28 123 123
GRB2/SOS1/SHC 0.03 0.019 -10000 0 -0.27 1 1
HRAS 0.015 0 -10000 0 -10000 0 0
IRS1/Crk -0.11 0.16 -10000 0 -0.28 121 121
IGF-1R heterotetramer/IGF1/PTP1B -0.15 0.16 -10000 0 -0.32 121 121
AKT1 -0.075 0.14 -10000 0 -0.45 5 5
BAD -0.064 0.13 -10000 0 -0.42 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.11 0.16 -10000 0 -0.28 121 121
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.12 0.16 -10000 0 -0.28 121 121
RAF1 -0.056 0.13 -10000 0 -0.39 5 5
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.1 0.15 -10000 0 -0.26 121 121
YWHAZ 0.015 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.13 0.17 -10000 0 -0.32 124 124
PIK3CA 0.015 0 -10000 0 -10000 0 0
RPS6KB1 -0.075 0.14 -10000 0 -0.45 5 5
GNB2L1 0.015 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.051 0.11 -10000 0 -0.34 5 5
PXN 0.015 0 -10000 0 -10000 0 0
PIK3R1 0.015 0 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.022 0 -10000 0 -10000 0 0
HRAS/GTP -0.1 0.12 -10000 0 -0.45 6 6
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.086 0.15 -10000 0 -0.4 6 6
IGF-1R heterotetramer -0.023 0.066 -10000 0 -0.65 2 2
IGF-1R heterotetramer/IGF1/IRS/Nck -0.11 0.16 -10000 0 -0.28 121 121
Crk/p130 Cas/Paxillin -0.088 0.15 -10000 0 -0.49 5 5
IGF1R -0.023 0.066 -10000 0 -0.65 2 2
IGF1 -0.25 0.3 -10000 0 -0.58 121 121
IRS2/Crk -0.11 0.17 -10000 0 -0.53 14 14
PI3K -0.099 0.15 -10000 0 -0.51 5 5
apoptosis 0.049 0.12 0.36 5 -10000 0 5
HRAS/GDP 0.011 0 -10000 0 -10000 0 0
PRKCD -0.14 0.21 -10000 0 -0.37 121 121
RAF1/14-3-3 E -0.042 0.12 -10000 0 -0.34 6 6
BAD/14-3-3 -0.051 0.12 -10000 0 -0.38 5 5
PRKCZ -0.076 0.14 -10000 0 -0.46 6 6
Crk/p130 Cas/Paxillin/FAK1 -0.08 0.091 -10000 0 -0.37 5 5
PTPN1 0.015 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.16 0.22 -10000 0 -0.39 121 121
BCAR1 0.015 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.1 0.16 -10000 0 -0.28 121 121
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.015 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.11 0.16 -10000 0 -0.28 121 121
GRB10 0.013 0.036 -10000 0 -0.57 1 1
PTPN11 -0.11 0.16 -10000 0 -0.28 121 121
IRS1 -0.13 0.17 -10000 0 -0.31 124 124
IRS2 -0.12 0.18 -10000 0 -0.31 121 121
IGF-1R heterotetramer/IGF1 -0.18 0.23 -10000 0 -0.43 121 121
GRB2 0.015 0 -10000 0 -10000 0 0
PDPK1 -0.087 0.14 -10000 0 -0.48 5 5
YWHAE 0.013 0.036 -10000 0 -0.57 1 1
PRKD1 -0.16 0.23 -10000 0 -0.4 121 121
SHC1 0.013 0.03 -10000 0 -0.48 1 1
Reelin signaling pathway

Figure S13.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S13.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.001 0.085 -9999 0 -0.34 16 16
VLDLR -0.002 0.099 -9999 0 -0.57 8 8
CRKL 0.011 0.043 -9999 0 -0.48 2 2
LRPAP1 0.013 0.03 -9999 0 -0.48 1 1
FYN 0.009 0.061 -9999 0 -0.57 3 3
ITGA3 0.009 0.053 -9999 0 -0.48 3 3
RELN/VLDLR/Fyn -0.11 0.18 -9999 0 -0.34 101 101
MAPK8IP1/MKK7/MAP3K11/JNK1 0.039 0.042 -9999 0 -10000 0 0
AKT1 -0.091 0.16 -9999 0 -0.44 18 18
MAP2K7 0.015 0 -9999 0 -10000 0 0
RAPGEF1 0.015 0 -9999 0 -10000 0 0
DAB1 -0.07 0.19 -9999 0 -0.53 39 39
RELN/LRP8/DAB1 -0.18 0.22 -9999 0 -0.37 140 140
LRPAP1/LRP8 -0.042 0.14 -9999 0 -0.34 48 48
RELN/LRP8/DAB1/Fyn -0.17 0.21 -9999 0 -0.37 111 111
DAB1/alpha3/beta1 Integrin -0.17 0.18 -9999 0 -0.5 45 45
long-term memory -0.21 0.25 -9999 0 -0.59 64 64
DAB1/LIS1 -0.17 0.19 -9999 0 -0.52 44 44
DAB1/CRLK/C3G -0.16 0.18 -9999 0 -0.5 45 45
PIK3CA 0.015 0 -9999 0 -10000 0 0
DAB1/NCK2 -0.17 0.19 -9999 0 -0.52 44 44
ARHGEF2 0.015 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.1 0.23 -9999 0 -0.56 52 52
CDK5R1 -0.015 0.12 -9999 0 -0.48 16 16
RELN -0.19 0.27 -9999 0 -0.56 93 93
PIK3R1 0.015 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.15 0.21 -9999 0 -0.37 122 122
GRIN2A/RELN/LRP8/DAB1/Fyn -0.22 0.26 -9999 0 -0.62 61 61
MAPK8 0.009 0.061 -9999 0 -0.57 3 3
RELN/VLDLR/DAB1 -0.14 0.2 -9999 0 -0.35 122 122
ITGB1 0.015 0 -9999 0 -10000 0 0
MAP1B -0.19 0.23 -9999 0 -0.41 117 117
RELN/LRP8 -0.15 0.21 -9999 0 -0.37 120 120
GRIN2B/RELN/LRP8/DAB1/Fyn -0.17 0.21 -9999 0 -0.55 39 39
PI3K 0.022 0 -9999 0 -10000 0 0
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin 0.018 0.038 -9999 0 -0.34 3 3
RAP1A -0.12 0.2 -9999 0 -0.46 45 45
PAFAH1B1 0.015 0 -9999 0 -10000 0 0
MAPK8IP1 0.011 0.047 -9999 0 -0.52 2 2
CRLK/C3G 0.02 0.031 -9999 0 -0.34 2 2
GRIN2B -0.009 0.084 -9999 0 -0.48 8 8
NCK2 0.015 0 -9999 0 -10000 0 0
neuron differentiation -0.074 0.13 -9999 0 -0.31 37 37
neuron adhesion -0.11 0.19 -9999 0 -0.43 46 46
LRP8 -0.073 0.19 -9999 0 -0.48 47 47
GSK3B -0.078 0.15 -9999 0 -0.41 18 18
RELN/VLDLR/DAB1/Fyn -0.13 0.19 -9999 0 -0.33 113 113
MAP3K11 0.015 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.1 0.16 -9999 0 -0.28 110 110
CDK5 0.015 0 -9999 0 -10000 0 0
MAPT -0.021 0.15 -9999 0 -0.51 23 23
neuron migration -0.13 0.21 -9999 0 -0.45 47 47
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.074 0.13 -9999 0 -0.31 37 37
RELN/VLDLR -0.14 0.2 -9999 0 -0.37 97 97
p75(NTR)-mediated signaling

Figure S14.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S14.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.022 0 -10000 0 -10000 0 0
Necdin/E2F1 -0.12 0.21 -10000 0 -0.4 88 88
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.075 0.19 -10000 0 -0.33 82 82
NGF (dimer)/p75(NTR)/BEX1 -0.14 0.24 -10000 0 -0.42 99 99
NT-4/5 (dimer)/p75(NTR) -0.11 0.22 -10000 0 -0.44 78 78
IKBKB 0.015 0 -10000 0 -10000 0 0
AKT1 -0.072 0.18 -10000 0 -0.56 14 14
IKBKG 0.015 0 -10000 0 -10000 0 0
BDNF -0.094 0.23 -10000 0 -0.57 50 50
MGDIs/NGR/p75(NTR)/LINGO1 -0.11 0.19 -10000 0 -0.34 102 102
FURIN 0.013 0.03 -10000 0 -0.48 1 1
proBDNF (dimer)/p75(NTR)/Sortilin -0.12 0.21 -10000 0 -0.38 100 100
LINGO1 -0.007 0.1 -10000 0 -0.48 12 12
Sortilin/TRAF6/NRIF 0 0 -10000 0 -10000 0 0
proBDNF (dimer) -0.094 0.23 -10000 0 -0.56 50 50
NTRK1 0.006 0.061 -10000 0 -0.48 4 4
RTN4R -0.054 0.17 -10000 0 -0.48 37 37
neuron apoptosis -0.11 0.22 -10000 0 -0.5 41 41
IRAK1 0.015 0 -10000 0 -10000 0 0
SHC1 -0.1 0.21 -10000 0 -0.39 86 86
ARHGDIA 0.015 0 -10000 0 -10000 0 0
RhoA/GTP 0.011 0 -10000 0 -10000 0 0
Gamma Secretase 0.045 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.087 0.2 -10000 0 -0.36 82 82
MAGEH1 0.011 0.05 -10000 0 -0.57 2 2
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.13 0.24 -10000 0 -0.41 98 98
Mammalian IAPs/DIABLO 0.016 0.086 -10000 0 -0.31 15 15
proNGF (dimer) -0.061 0.2 -10000 0 -0.56 35 35
MAGED1 0.015 0 -10000 0 -10000 0 0
APP 0.011 0.05 -10000 0 -0.57 2 2
NT-4/5 (dimer) -0.033 0.16 -10000 0 -0.56 22 22
ZNF274 0.015 0 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.08 0.18 -10000 0 -0.33 82 82
NGF -0.062 0.2 -10000 0 -0.57 35 35
cell cycle arrest -0.086 0.16 -10000 0 -0.55 14 14
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.059 0.16 -10000 0 -0.44 18 18
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.087 0.19 -10000 0 -0.37 78 78
NCSTN 0.015 0 -10000 0 -10000 0 0
mol:GTP -0.11 0.21 -10000 0 -0.38 88 88
PSENEN 0.015 0 -10000 0 -10000 0 0
mol:ceramide -0.085 0.19 -10000 0 -0.35 82 82
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.039 0.14 -10000 0 -0.42 15 15
p75(NTR)/beta APP -0.084 0.19 -10000 0 -0.41 66 66
BEX1 -0.04 0.16 -10000 0 -0.55 25 25
mol:GDP -0.11 0.2 -10000 0 -0.39 86 86
NGF (dimer) -0.083 0.16 -10000 0 -0.34 49 49
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.092 0.18 -10000 0 -0.34 66 66
PIK3R1 0.015 0 -10000 0 -10000 0 0
RAC1/GTP -0.089 0.18 -10000 0 -0.33 86 86
MYD88 0.015 0 -10000 0 -10000 0 0
CHUK 0.015 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.11 0.21 -10000 0 -0.38 88 88
RHOB 0.015 0 -10000 0 -10000 0 0
RHOA 0.015 0 -10000 0 -10000 0 0
MAGE-G1/E2F1 -0.061 0.15 -10000 0 -0.34 62 62
NT3 (dimer) -0.096 0.23 -10000 0 -0.56 51 51
TP53 -0.077 0.18 -10000 0 -0.53 15 15
PRDM4 -0.085 0.19 -10000 0 -0.35 82 82
BDNF (dimer) -0.16 0.21 -10000 0 -0.35 131 131
PIK3CA 0.015 0 -10000 0 -10000 0 0
SORT1 0.015 0 -10000 0 -10000 0 0
activation of caspase activity -0.1 0.17 -10000 0 -0.52 20 20
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.085 0.19 -10000 0 -0.35 82 82
RHOC 0.015 0 -10000 0 -10000 0 0
XIAP 0.013 0.03 -10000 0 -0.48 1 1
MAPK10 -0.11 0.22 -10000 0 -0.51 40 40
DIABLO 0.015 0 -10000 0 -10000 0 0
SMPD2 -0.085 0.19 -10000 0 -0.35 82 82
APH1B 0.015 0 -10000 0 -10000 0 0
APH1A 0.015 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.1 0.21 -10000 0 -0.39 86 86
PSEN1 0.015 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.022 0 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.16 0.24 -10000 0 -0.45 101 101
MAPK8 -0.086 0.21 -10000 0 -0.51 31 31
MAPK9 -0.083 0.21 -10000 0 -0.51 31 31
APAF1 0.015 0 -10000 0 -10000 0 0
NTF3 -0.096 0.23 -10000 0 -0.56 51 51
NTF4 -0.033 0.16 -10000 0 -0.57 22 22
NDN -0.065 0.2 -10000 0 -0.57 37 37
RAC1/GDP 0.011 0 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.095 0.15 -10000 0 -0.53 14 14
p75 CTF/Sortilin/TRAF6/NRIF 0.039 0 -10000 0 -10000 0 0
RhoA-B-C/GTP -0.13 0.19 -10000 0 -0.38 88 88
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.089 0.19 -10000 0 -0.57 15 15
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.1 0.2 -10000 0 -0.34 96 96
PRKACB 0.011 0.05 -10000 0 -0.57 2 2
proBDNF (dimer)/p75 ECD -0.058 0.17 -10000 0 -0.41 50 50
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.019 0.14 -10000 0 -0.56 16 16
BIRC2 0.011 0.043 -10000 0 -0.48 2 2
neuron projection morphogenesis -0.12 0.2 0.2 8 -0.4 77 85
BAD -0.087 0.21 -10000 0 -0.48 37 37
RIPK2 0.015 0 -10000 0 -10000 0 0
NGFR -0.12 0.25 -10000 0 -0.56 65 65
CYCS -0.072 0.18 -10000 0 -0.32 82 82
ADAM17 0.015 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.085 0.19 -10000 0 -0.35 82 82
BCL2L11 -0.087 0.21 -10000 0 -0.48 37 37
BDNF (dimer)/p75(NTR) -0.16 0.24 -10000 0 -0.45 100 100
PI3K -0.084 0.19 -10000 0 -0.35 82 82
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.085 0.19 -10000 0 -0.35 82 82
NDNL2 0.015 0 -10000 0 -10000 0 0
YWHAE 0.013 0.036 -10000 0 -0.57 1 1
PRKCI 0.015 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.13 0.24 -10000 0 -0.46 86 86
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.085 0.19 -10000 0 -0.35 82 82
TRAF6 0.015 0 -10000 0 -10000 0 0
RAC1 0.015 0 -10000 0 -10000 0 0
PRKCZ 0.013 0.036 -10000 0 -0.57 1 1
PLG -0.001 0.042 -10000 0 -0.48 2 2
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.14 0.24 -10000 0 -0.39 109 109
SQSTM1 0.015 0 -10000 0 -10000 0 0
NGFRAP1 0.011 0.05 -10000 0 -0.57 2 2
CASP3 -0.078 0.19 -10000 0 -0.44 37 37
E2F1 -0.1 0.21 -10000 0 -0.48 62 62
CASP9 0.015 0 -10000 0 -10000 0 0
IKK complex -0.075 0.13 -10000 0 -0.43 21 21
NGF (dimer)/TRKA -0.041 0.15 -10000 0 -0.4 39 39
MMP7 -0.1 0.22 -10000 0 -0.5 62 62
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.072 0.18 -10000 0 -0.32 82 82
MMP3 -0.1 0.22 -10000 0 -0.53 57 57
APAF-1/Caspase 9 -0.083 0.13 -10000 0 -0.42 22 22
Aurora C signaling

Figure S15.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S15.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.013 0.03 -9999 0 -0.48 1 1
Aurora C/Aurora B/INCENP -0.1 0.14 -9999 0 -0.25 126 126
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.033 0.035 -9999 0 -10000 0 0
AURKB -0.21 0.25 -9999 0 -0.48 120 120
AURKC 0 0.085 -9999 0 -0.48 8 8
TCGA08_retinoblastoma

Figure S16.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S16.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2B -0.033 0.15 -10000 0 -0.52 24 24
CDKN2C 0.037 0.04 -10000 0 -0.43 1 1
CDKN2A -0.23 0.26 -10000 0 -0.5 127 127
CCND2 0.048 0.081 0.23 24 -0.15 9 33
RB1 -0.045 0.088 0.16 2 -0.23 24 26
CDK4 0.063 0.081 0.24 25 -10000 0 25
CDK6 0.052 0.091 0.25 24 -0.18 8 32
G1/S progression 0.045 0.087 0.23 24 -0.16 2 26
Thromboxane A2 receptor signaling

Figure S17.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S17.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 -0.016 0.13 -10000 0 -0.53 15 15
GNB1/GNG2 -0.075 0.089 -10000 0 -0.18 102 102
AKT1 -0.035 0.13 -10000 0 -0.2 73 73
EGF -0.014 0.11 -10000 0 -0.48 15 15
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.035 0.057 -10000 0 -0.37 1 1
mol:Ca2+ -0.075 0.18 -10000 0 -0.3 100 100
LYN 0.036 0.055 -10000 0 -0.37 1 1
RhoA/GTP -0.048 0.058 -10000 0 -0.13 39 39
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.086 0.21 -10000 0 -0.34 101 101
GNG2 0.009 0.061 -10000 0 -0.57 3 3
ARRB2 0.015 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.011 0.072 -10000 0 -0.34 3 3
G beta5/gamma2 -0.096 0.12 -10000 0 -0.24 102 102
PRKCH -0.088 0.2 -10000 0 -0.34 100 100
DNM1 0.004 0.079 -10000 0 -0.57 5 5
TXA2/TP beta/beta Arrestin3 -0.006 0.033 -10000 0 -0.27 1 1
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR -0.015 0.12 -10000 0 -0.57 13 13
G12 family/GTP -0.12 0.14 -10000 0 -0.3 100 100
ADRBK1 0.015 0 -10000 0 -10000 0 0
ADRBK2 0.011 0.047 -10000 0 -0.52 2 2
RhoA/GTP/ROCK1 0.012 0.01 -10000 0 -10000 0 0
mol:GDP 0.032 0.12 0.28 13 -10000 0 13
mol:NADP 0.013 0.03 -10000 0 -0.48 1 1
RAB11A 0.015 0 -10000 0 -10000 0 0
PRKG1 -0.11 0.24 -10000 0 -0.57 58 58
mol:IP3 -0.1 0.22 -10000 0 -0.38 100 100
cell morphogenesis 0.011 0.011 -10000 0 -10000 0 0
PLCB2 -0.15 0.29 -10000 0 -0.51 100 100
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.002 0.097 -10000 0 -0.39 3 3
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.025 0.082 -10000 0 -0.4 4 4
RHOA 0.015 0 -10000 0 -10000 0 0
PTGIR 0.013 0.036 -10000 0 -0.57 1 1
PRKCB1 -0.1 0.22 -10000 0 -0.37 101 101
GNAQ 0.015 0 -10000 0 -10000 0 0
mol:L-citrulline 0.013 0.03 -10000 0 -0.48 1 1
TXA2/TXA2-R family -0.16 0.3 -10000 0 -0.53 100 100
LCK 0.031 0.067 -10000 0 -0.39 2 2
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.011 0.048 -10000 0 -10000 0 0
TXA2-R family/G12 family/GDP/G beta/gamma 0.031 0.027 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.011 0.046 -10000 0 -10000 0 0
MAPK14 -0.045 0.14 -10000 0 -0.22 100 100
TGM2/GTP -0.12 0.25 -10000 0 -0.43 100 100
MAPK11 -0.045 0.14 -10000 0 -0.22 100 100
ARHGEF1 -0.035 0.11 -10000 0 -0.17 100 100
GNAI2 0.015 0 -10000 0 -10000 0 0
JNK cascade -0.1 0.23 -10000 0 -0.39 100 100
RAB11/GDP 0.015 0.002 -10000 0 -10000 0 0
ICAM1 -0.068 0.17 -10000 0 -0.28 102 102
cAMP biosynthetic process -0.097 0.21 -10000 0 -0.36 100 100
Gq family/GTP/EBP50 -0.008 0.085 -10000 0 -0.26 6 6
actin cytoskeleton reorganization 0.011 0.011 -10000 0 -10000 0 0
SRC 0.036 0.055 -10000 0 -0.37 1 1
GNB5 0.015 0 -10000 0 -10000 0 0
GNB1 0.015 0 -10000 0 -10000 0 0
EGF/EGFR 0.033 0.076 -10000 0 -0.28 3 3
VCAM1 -0.078 0.18 -10000 0 -0.3 100 100
TP beta/Gq family/GDP/G beta5/gamma2 0.011 0.072 -10000 0 -0.34 3 3
platelet activation -0.062 0.19 -10000 0 -0.3 100 100
PGI2/IP 0.008 0.026 -10000 0 -0.42 1 1
PRKACA 0.008 0.065 -10000 0 -0.27 14 14
Gq family/GDP/G beta5/gamma2 0.009 0.072 -10000 0 -0.31 3 3
TXA2/TP beta/beta Arrestin2 -0.011 0.072 -10000 0 -0.53 5 5
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.015 0.064 -10000 0 -0.24 15 15
mol:DAG -0.12 0.24 -10000 0 -0.42 101 101
EGFR -0.007 0.11 -10000 0 -0.52 11 11
TXA2/TP alpha -0.14 0.28 -10000 0 -0.48 100 100
Gq family/GTP -0.037 0.087 -10000 0 -0.23 46 46
YES1 0.036 0.055 -10000 0 -0.37 1 1
GNAI2/GTP -0.012 0.05 -10000 0 -0.43 1 1
PGD2/DP -0.012 0.092 -10000 0 -0.42 13 13
SLC9A3R1 -0.002 0.09 -10000 0 -0.48 9 9
FYN 0.033 0.064 -10000 0 -0.39 2 2
mol:NO 0.013 0.03 -10000 0 -0.48 1 1
GNA15 0.011 0.05 -10000 0 -0.57 2 2
PGK/cGMP -0.061 0.15 -10000 0 -0.35 59 59
RhoA/GDP 0.015 0.002 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.02 0.094 -10000 0 -0.49 3 3
NOS3 0.013 0.03 -10000 0 -0.48 1 1
RAC1 0.015 0 -10000 0 -10000 0 0
PRKCA -0.089 0.2 -10000 0 -0.34 100 100
PRKCB -0.14 0.24 -10000 0 -0.42 103 103
PRKCE -0.085 0.2 -10000 0 -0.34 100 100
PRKCD -0.1 0.22 -10000 0 -0.38 100 100
PRKCG -0.11 0.23 -10000 0 -0.39 100 100
muscle contraction -0.14 0.28 -10000 0 -0.49 100 100
PRKCZ -0.086 0.21 -10000 0 -0.34 100 100
ARR3 0.003 0.006 -10000 0 -10000 0 0
TXA2/TP beta 0.012 0.066 -10000 0 -0.48 1 1
PRKCQ -0.1 0.22 -10000 0 -0.37 101 101
MAPKKK cascade -0.13 0.27 -10000 0 -0.46 100 100
SELE -0.12 0.23 -10000 0 -0.41 102 102
TP beta/GNAI2/GDP/G beta/gamma 0.034 0.063 -10000 0 -10000 0 0
ROCK1 0.015 0 -10000 0 -10000 0 0
GNA14 -0.079 0.21 -10000 0 -0.57 43 43
chemotaxis -0.19 0.34 -10000 0 -0.62 100 100
GNA12 0.015 0 -10000 0 -10000 0 0
GNA13 0.015 0 -10000 0 -10000 0 0
GNA11 0.013 0.036 -10000 0 -0.57 1 1
Rac1/GTP 0.007 0.006 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

Figure S18.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S18.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.18 0.42 -9999 0 -0.87 47 47
HDAC7 0.017 0.001 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.12 0.35 -9999 0 -0.73 36 36
SMAD4 0.017 0 -9999 0 -10000 0 0
ID2 -0.18 0.43 -9999 0 -0.89 46 46
AP1 -0.11 0.22 -9999 0 -0.43 81 81
ABCG2 -0.19 0.44 -9999 0 -0.92 45 45
HIF1A -0.014 0.083 -9999 0 -0.63 1 1
TFF3 -0.26 0.49 -9999 0 -0.99 57 57
GATA2 -0.007 0.11 -9999 0 -0.52 12 12
AKT1 -0.013 0.088 -9999 0 -10000 0 0
response to hypoxia -0.036 0.093 -9999 0 -0.22 11 11
MCL1 -0.18 0.42 -9999 0 -0.88 45 45
NDRG1 -0.18 0.43 -9999 0 -0.89 45 45
SERPINE1 -0.18 0.43 -9999 0 -0.89 46 46
FECH -0.18 0.42 -9999 0 -0.88 45 45
FURIN -0.18 0.43 -9999 0 -0.9 42 42
NCOA2 -0.02 0.14 -9999 0 -0.57 16 16
EP300 -0.004 0.13 -9999 0 -0.33 15 15
HMOX1 -0.18 0.43 -9999 0 -0.9 42 42
BHLHE40 -0.18 0.43 -9999 0 -0.91 42 42
BHLHE41 -0.19 0.44 -9999 0 -0.9 46 46
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.01 0.09 -9999 0 -0.39 1 1
ENG 0.033 0.097 -9999 0 -0.35 1 1
JUN 0.001 0.093 -9999 0 -0.56 7 7
RORA -0.18 0.43 -9999 0 -0.9 45 45
ABCB1 -0.18 0.38 -9999 0 -1.2 31 31
TFRC -0.18 0.43 -9999 0 -0.89 47 47
CXCR4 -0.18 0.43 -9999 0 -0.89 46 46
TF -0.21 0.45 -9999 0 -0.92 51 51
CITED2 -0.18 0.42 -9999 0 -0.88 46 46
HIF1A/ARNT -0.18 0.5 -9999 0 -0.96 51 51
LDHA -0.023 0.044 -9999 0 -10000 0 0
ETS1 -0.18 0.42 -9999 0 -0.88 45 45
PGK1 -0.18 0.42 -9999 0 -0.9 42 42
NOS2 -0.2 0.45 -9999 0 -0.94 47 47
ITGB2 -0.19 0.44 -9999 0 -0.89 47 47
ALDOA -0.18 0.42 -9999 0 -0.89 43 43
Cbp/p300/CITED2 -0.16 0.45 -9999 0 -0.95 40 40
FOS -0.16 0.27 -9999 0 -0.56 80 80
HK2 -0.18 0.43 -9999 0 -0.9 43 43
SP1 0.017 0.029 -9999 0 -10000 0 0
GCK -0.074 0.38 -9999 0 -1.4 16 16
HK1 -0.18 0.42 -9999 0 -0.88 46 46
NPM1 -0.18 0.42 -9999 0 -0.88 46 46
EGLN1 -0.18 0.42 -9999 0 -0.89 43 43
CREB1 0.024 0 -9999 0 -10000 0 0
PGM1 -0.18 0.42 -9999 0 -0.88 45 45
SMAD3 0.017 0 -9999 0 -10000 0 0
EDN1 -0.052 0.22 -9999 0 -0.79 8 8
IGFBP1 -0.2 0.44 -9999 0 -0.89 48 48
VEGFA -0.075 0.32 -9999 0 -0.67 25 25
HIF1A/JAB1 -0.006 0.045 -9999 0 -0.46 1 1
CP -0.27 0.48 -9999 0 -0.97 61 61
CXCL12 -0.27 0.51 -9999 0 -0.96 72 72
COPS5 0.015 0.005 -9999 0 -10000 0 0
SMAD3/SMAD4 0.024 0.005 -9999 0 -10000 0 0
BNIP3 -0.18 0.43 -9999 0 -0.88 46 46
EGLN3 -0.18 0.43 -9999 0 -0.89 45 45
CA9 -0.33 0.49 -9999 0 -0.98 65 65
TERT -0.26 0.47 -9999 0 -0.98 53 53
ENO1 -0.18 0.42 -9999 0 -0.88 46 46
PFKL -0.18 0.42 -9999 0 -0.88 45 45
NCOA1 0.015 0.002 -9999 0 -10000 0 0
ADM -0.18 0.43 -9999 0 -0.89 45 45
ARNT -0.011 0.074 -9999 0 -10000 0 0
HNF4A -0.04 0.15 -9999 0 -0.49 27 27
ADFP -0.19 0.42 -9999 0 -0.87 50 50
SLC2A1 -0.076 0.33 -9999 0 -0.68 25 25
LEP -0.22 0.45 -9999 0 -0.94 52 52
HIF1A/ARNT/Cbp/p300 -0.12 0.37 -9999 0 -0.75 38 38
EPO -0.089 0.3 -9999 0 -0.71 13 13
CREBBP -0.004 0.13 -9999 0 -0.33 15 15
HIF1A/ARNT/Cbp/p300/HDAC7 -0.11 0.35 -9999 0 -0.73 35 35
PFKFB3 -0.18 0.43 -9999 0 -0.89 45 45
NT5E -0.2 0.46 -9999 0 -0.93 51 51
PLK1 signaling events

Figure S19.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S19.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0.049 0.062 0.12 89 -10000 0 89
BUB1B -0.072 0.11 -10000 0 -0.21 91 91
PLK1 -0.02 0.049 -10000 0 -0.099 53 53
PLK1S1 -0.003 0.025 -10000 0 -0.094 1 1
KIF2A -0.008 0.044 -10000 0 -0.17 1 1
regulation of mitotic centrosome separation -0.019 0.048 -10000 0 -0.099 53 53
GOLGA2 0.015 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.16 0.22 -10000 0 -0.39 118 118
WEE1 -0.016 0.052 -10000 0 -10000 0 0
cytokinesis -0.13 0.1 -10000 0 -0.23 88 88
PP2A-alpha B56 0.02 0.032 -10000 0 -10000 0 0
AURKA -0.017 0.044 -10000 0 -0.13 1 1
PICH/PLK1 -0.1 0.18 -10000 0 -0.35 77 77
CENPE -0.067 0.14 -10000 0 -0.31 59 59
RhoA/GTP 0.011 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.008 0.043 -10000 0 -0.17 1 1
PPP2CA 0.015 0 -10000 0 -10000 0 0
FZR1 0.015 0 -10000 0 -10000 0 0
TPX2 -0.034 0.046 -10000 0 -0.14 1 1
PAK1 0.012 0.036 -10000 0 -0.58 1 1
SPC24 -0.14 0.23 -10000 0 -0.48 85 85
FBXW11 0.015 0 -10000 0 -10000 0 0
CLSPN -0.032 0.051 -10000 0 -0.11 39 39
GORASP1 0.015 0 -10000 0 -10000 0 0
metaphase -0.002 0.004 -10000 0 -0.01 51 51
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.01 0.025 -10000 0 -0.051 53 53
G2 phase of mitotic cell cycle -0.002 0.003 -10000 0 -0.009 1 1
STAG2 0.015 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.006 0.011 -10000 0 -10000 0 0
spindle elongation -0.019 0.048 -10000 0 -0.099 53 53
ODF2 0.013 0.003 -10000 0 -10000 0 0
BUB1 -0.012 0.028 -10000 0 -10000 0 0
TPT1 -0.003 0.025 -10000 0 -10000 0 0
CDC25C -0.048 0.053 -10000 0 -10000 0 0
CDC25B 0.002 0.074 -10000 0 -0.49 6 6
SGOL1 -0.049 0.062 -10000 0 -0.12 89 89
RHOA 0.015 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.073 0.1 -10000 0 -0.24 36 36
CDC14B 0.01 0.027 -10000 0 -0.42 1 1
CDC20 -0.28 0.24 -10000 0 -0.48 159 159
PLK1/PBIP1 -0.03 0.056 -10000 0 -0.26 10 10
mitosis -0.002 0.01 0.019 19 -0.017 60 79
FBXO5 -0.011 0.047 -10000 0 -0.22 3 3
CDC2 -0.003 0.005 -10000 0 -0.011 38 38
NDC80 -0.15 0.24 -10000 0 -0.48 90 90
metaphase plate congression -0.008 0.031 -10000 0 -10000 0 0
ERCC6L -0.091 0.17 -10000 0 -0.38 46 46
NLP/gamma Tubulin -0.006 0.026 -10000 0 -0.092 2 2
microtubule cytoskeleton organization -0.003 0.025 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint -0.001 0.002 -10000 0 -10000 0 0
PPP1R12A 0.014 0.001 -10000 0 -10000 0 0
interphase -0.001 0.002 -10000 0 -10000 0 0
PLK1/PRC1-2 -0.23 0.19 -10000 0 -0.33 197 197
GRASP65/GM130/RAB1/GTP/PLK1 -0.01 0.025 -10000 0 -10000 0 0
RAB1A 0.015 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA -0.014 0.047 -10000 0 -0.2 2 2
mitotic prometaphase -0.002 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.015 0.048 -10000 0 -0.29 1 1
microtubule-based process -0.2 0.14 -10000 0 -0.28 196 196
Golgi organization -0.019 0.048 -10000 0 -0.099 53 53
Cohesin/SA2 -0.023 0.033 -10000 0 -0.16 1 1
PPP1CB/MYPT1 0.017 0.009 -10000 0 -10000 0 0
KIF20A -0.35 0.22 -10000 0 -0.48 196 196
APC/C/CDC20 -0.17 0.16 -10000 0 -0.3 159 159
PPP2R1A 0.015 0 -10000 0 -10000 0 0
chromosome segregation -0.03 0.055 -10000 0 -0.26 10 10
PRC1 -0.086 0.2 -10000 0 -0.48 54 54
ECT2 -0.037 0.11 -10000 0 -0.32 30 30
C13orf34 -0.011 0.044 -10000 0 -0.21 2 2
NUDC -0.008 0.031 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore -0.071 0.11 -10000 0 -0.21 91 91
spindle assembly -0.012 0.038 -10000 0 -0.095 7 7
spindle stabilization -0.003 0.025 -10000 0 -0.093 1 1
APC/C/HCDH1 0.018 0.023 -10000 0 -0.35 1 1
MKLP2/PLK1 -0.2 0.14 -10000 0 -0.29 196 196
CCNB1 -0.16 0.24 -10000 0 -0.48 96 96
PPP1CB 0.014 0.001 -10000 0 -10000 0 0
BTRC 0.015 0 -10000 0 -10000 0 0
ROCK2 -0.009 0.071 -10000 0 -0.43 6 6
TUBG1 -0.003 0.025 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.073 0.099 -10000 0 -0.25 30 30
MLF1IP -0.004 0.066 -10000 0 -0.36 9 9
INCENP 0.013 0.03 -10000 0 -0.48 1 1
Plasma membrane estrogen receptor signaling

Figure S20.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S20.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.024 0.13 -10000 0 -0.29 48 48
ER alpha/Gai/GDP/Gbeta gamma -0.18 0.34 -10000 0 -0.55 97 97
AKT1 -0.14 0.36 -10000 0 -0.9 47 47
PIK3CA 0.015 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.14 0.36 -10000 0 -0.92 47 47
mol:Ca2+ -0.05 0.19 -10000 0 -0.43 46 46
IGF1R 0.011 0.05 -10000 0 -0.57 2 2
E2/ER alpha (dimer)/Striatin -0.044 0.14 -10000 0 -0.35 47 47
SHC1 0.013 0.03 -10000 0 -0.48 1 1
apoptosis 0.13 0.34 0.84 47 -10000 0 47
RhoA/GTP -0.042 0.093 -10000 0 -0.46 1 1
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.17 0.25 -10000 0 -0.54 71 71
regulation of stress fiber formation -0.008 0.1 0.39 4 -10000 0 4
E2/ERA-ERB (dimer) -0.045 0.14 -10000 0 -0.34 48 48
KRAS 0.013 0.03 -10000 0 -0.48 1 1
G13/GTP -0.039 0.13 -10000 0 -0.31 47 47
pseudopodium formation 0.008 0.1 -10000 0 -0.39 4 4
E2/ER alpha (dimer)/PELP1 -0.044 0.14 -10000 0 -0.35 47 47
GRB2 0.015 0 -10000 0 -10000 0 0
GNG2 0.009 0.061 -10000 0 -0.57 3 3
GNAO1 -0.16 0.27 -10000 0 -0.57 80 80
HRAS 0.015 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.12 0.29 -10000 0 -0.69 47 47
E2/ER beta (dimer) 0.01 0.022 -10000 0 -0.35 1 1
mol:GDP -0.07 0.15 -10000 0 -0.39 47 47
mol:NADP -0.12 0.29 -10000 0 -0.69 47 47
PIK3R1 0.015 0 -10000 0 -10000 0 0
mol:IP3 -0.053 0.2 -10000 0 -0.44 46 46
IGF-1R heterotetramer 0.011 0.05 -10000 0 -0.56 2 2
PLCB1 -0.062 0.2 -10000 0 -0.46 46 46
PLCB2 -0.055 0.19 -10000 0 -0.44 45 45
IGF1 -0.25 0.29 -10000 0 -0.57 121 121
mol:L-citrulline -0.12 0.29 -10000 0 -0.69 47 47
RHOA 0.015 0 -10000 0 -10000 0 0
Gai/GDP -0.25 0.41 -10000 0 -0.84 80 80
JNK cascade 0.01 0.022 -10000 0 -0.35 1 1
BCAR1 0.015 0 -10000 0 -10000 0 0
ESR2 0.013 0.03 -10000 0 -0.48 1 1
GNAQ 0.015 0 -10000 0 -10000 0 0
ESR1 -0.087 0.22 -10000 0 -0.57 47 47
Gq family/GDP/Gbeta gamma -0.007 0.11 -10000 0 -0.47 3 3
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.028 0.12 -10000 0 -0.3 30 30
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.17 0.25 -10000 0 -0.54 72 72
GNAZ -0.12 0.24 -10000 0 -0.57 60 60
E2/ER alpha (dimer) -0.064 0.16 -10000 0 -0.42 47 47
STRN 0.015 0 -10000 0 -10000 0 0
GNAL -0.23 0.29 -10000 0 -0.57 112 112
PELP1 0.015 0 -10000 0 -10000 0 0
MAPK11 0.02 0.019 -10000 0 -0.28 1 1
GNAI2 0.015 0 -10000 0 -10000 0 0
GNAI3 0.015 0 -10000 0 -10000 0 0
GNAI1 0.013 0.036 -10000 0 -0.57 1 1
HBEGF -0.19 0.3 -10000 0 -0.6 73 73
cAMP biosynthetic process -0.16 0.18 -10000 0 -0.33 131 131
SRC -0.16 0.32 -10000 0 -0.61 71 71
PI3K 0.022 0 -10000 0 -10000 0 0
GNB1 0.015 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.062 0.13 -10000 0 -0.34 47 47
SOS1 0.015 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.22 0.24 -10000 0 -0.48 106 106
Gs family/GTP -0.17 0.19 -10000 0 -0.34 131 131
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.028 0.017 -10000 0 -0.25 1 1
vasodilation -0.11 0.27 -10000 0 -0.65 47 47
mol:DAG -0.053 0.2 -10000 0 -0.44 46 46
Gs family/GDP/Gbeta gamma -0.15 0.18 -10000 0 -0.46 49 49
MSN 0.007 0.11 -10000 0 -0.42 4 4
Gq family/GTP -0.065 0.19 -10000 0 -0.47 45 45
mol:PI-3-4-5-P3 -0.14 0.35 -10000 0 -0.88 47 47
NRAS 0.015 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.11 0.27 0.65 47 -10000 0 47
GRB2/SOS1 0.022 0 -10000 0 -10000 0 0
RhoA/GDP -0.065 0.14 -10000 0 -0.37 47 47
NOS3 -0.13 0.31 -10000 0 -0.75 47 47
GNA11 0.013 0.036 -10000 0 -0.57 1 1
MAPKKK cascade -0.11 0.29 -10000 0 -0.7 47 47
E2/ER alpha (dimer)/PELP1/Src -0.18 0.27 -10000 0 -0.57 71 71
ruffle organization 0.008 0.1 -10000 0 -0.39 4 4
ROCK2 -0.001 0.12 -10000 0 -0.46 3 3
GNA14 -0.079 0.21 -10000 0 -0.57 43 43
GNA15 0.011 0.05 -10000 0 -0.57 2 2
GNA13 0.015 0 -10000 0 -10000 0 0
MMP9 -0.21 0.29 -10000 0 -0.58 79 79
MMP2 -0.17 0.31 -10000 0 -0.58 78 78
Ephrin A reverse signaling

Figure S21.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S21.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.044 0.14 -9999 0 -0.35 43 43
EFNA5 0 0.093 -9999 0 -0.57 7 7
FYN -0.033 0.13 -9999 0 -0.31 46 46
neuron projection morphogenesis -0.044 0.14 -9999 0 -0.35 43 43
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.044 0.14 -9999 0 -0.35 43 43
EPHA5 -0.071 0.2 -9999 0 -0.56 37 37
Fc-epsilon receptor I signaling in mast cells

Figure S22.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S22.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PPAP2A 0.013 0.036 -9999 0 -0.57 1 1
LAT2 -0.093 0.19 -9999 0 -0.45 42 42
AP1 -0.18 0.22 -9999 0 -0.51 66 66
mol:PIP3 -0.11 0.23 -9999 0 -0.5 50 50
IKBKB -0.071 0.15 -9999 0 -0.29 65 65
AKT1 -0.069 0.18 -9999 0 -0.42 38 38
IKBKG -0.071 0.15 -9999 0 -0.29 64 64
MS4A2 -0.14 0.26 -9999 0 -0.57 70 70
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.014 0.001 -9999 0 -10000 0 0
MAP3K1 -0.065 0.18 -9999 0 -0.4 46 46
mol:Ca2+ -0.075 0.18 -9999 0 -0.37 50 50
LYN 0.013 0.005 -9999 0 -10000 0 0
CBLB -0.09 0.19 -9999 0 -0.43 44 44
SHC1 0.013 0.03 -9999 0 -0.48 1 1
RasGAP/p62DOK -0.067 0.15 -9999 0 -0.31 76 76
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0.002 0.086 -9999 0 -0.57 6 6
PLD2 -0.11 0.21 -9999 0 -0.51 40 40
PTPN13 -0.09 0.2 -9999 0 -0.47 40 40
PTPN11 0.011 0.009 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.041 0.16 -9999 0 -0.33 37 37
SYK 0.009 0.052 -9999 0 -0.59 2 2
GRB2 0.015 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.15 0.2 -9999 0 -0.51 50 50
LAT -0.091 0.19 -9999 0 -0.44 42 42
PAK2 -0.082 0.2 -9999 0 -0.45 46 46
NFATC2 -0.16 0.25 -9999 0 -0.48 74 74
HRAS -0.098 0.22 -9999 0 -0.49 47 47
GAB2 0.015 0 -9999 0 -10000 0 0
PLA2G1B 0.04 0.023 -9999 0 -10000 0 0
Fc epsilon R1 -0.18 0.23 -9999 0 -0.43 110 110
Antigen/IgE/Fc epsilon R1 -0.16 0.21 -9999 0 -0.39 110 110
mol:GDP -0.11 0.24 -9999 0 -0.53 47 47
JUN 0 0.093 -9999 0 -0.57 7 7
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.014 0.001 -9999 0 -10000 0 0
FOS -0.16 0.27 -9999 0 -0.57 80 80
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.1 0.2 -9999 0 -0.38 75 75
CHUK -0.071 0.15 -9999 0 -0.29 63 63
KLRG1 -0.087 0.18 -9999 0 -0.43 40 40
VAV1 -0.1 0.2 -9999 0 -0.45 50 50
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.09 0.19 -9999 0 -0.45 41 41
negative regulation of mast cell degranulation -0.08 0.18 -9999 0 -0.42 42 42
BTK -0.12 0.25 -9999 0 -0.58 45 45
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.14 0.27 -9999 0 -0.65 48 48
GAB2/PI3K/SHP2 -0.12 0.16 -9999 0 -0.46 38 38
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.11 0.21 -9999 0 -0.53 41 41
RAF1 0.028 0.028 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.17 0.23 -9999 0 -0.61 46 46
FCER1G -0.003 0.1 -9999 0 -0.5 11 11
FCER1A -0.13 0.25 -9999 0 -0.58 65 65
Antigen/IgE/Fc epsilon R1/Fyn -0.15 0.2 -9999 0 -0.42 76 76
MAPK3 0.039 0.023 -9999 0 -10000 0 0
MAPK1 0.039 0.023 -9999 0 -10000 0 0
NFKB1 0.015 0 -9999 0 -10000 0 0
MAPK8 -0.01 0.088 -9999 0 -0.59 3 3
DUSP1 -0.15 0.26 -9999 0 -0.57 76 76
NF-kappa-B/RelA -0.058 0.069 -9999 0 -0.2 21 21
actin cytoskeleton reorganization -0.094 0.2 -9999 0 -0.48 36 36
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.12 0.17 -9999 0 -0.45 45 45
FER -0.091 0.19 -9999 0 -0.45 41 41
RELA 0.015 0 -9999 0 -10000 0 0
ITK -0.075 0.15 -9999 0 -0.51 28 28
SOS1 0.015 0 -9999 0 -10000 0 0
PLCG1 -0.11 0.24 -9999 0 -0.53 46 46
cytokine secretion -0.043 0.05 -9999 0 -10000 0 0
SPHK1 -0.12 0.2 -9999 0 -0.45 52 52
PTK2 -0.098 0.2 -9999 0 -0.5 36 36
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.16 0.21 -9999 0 -0.54 50 50
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.1 0.23 -9999 0 -0.49 50 50
MAP2K2 0.034 0.024 -9999 0 -10000 0 0
MAP2K1 0.034 0.024 -9999 0 -10000 0 0
MAP2K7 0.015 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.1 0.15 -9999 0 -0.39 40 40
MAP2K4 0.018 0.012 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.18 0.24 -9999 0 -0.42 111 111
mol:Choline -0.11 0.2 -9999 0 -0.5 40 40
SHC/Grb2/SOS1 -0.11 0.16 -9999 0 -0.43 37 37
FYN 0.009 0.061 -9999 0 -0.57 3 3
DOK1 0.013 0.03 -9999 0 -0.48 1 1
PXN -0.084 0.19 -9999 0 -0.46 36 36
HCLS1 -0.091 0.19 -9999 0 -0.45 41 41
PRKCB -0.11 0.2 -9999 0 -0.41 69 69
FCGR2B -0.03 0.15 -9999 0 -0.56 21 21
IGHE -0.003 0.007 -9999 0 -10000 0 0
KLRG1/SHIP -0.081 0.18 -9999 0 -0.42 42 42
LCP2 0.013 0.036 -9999 0 -0.57 1 1
PLA2G4A -0.11 0.21 -9999 0 -0.46 52 52
RASA1 0.015 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.11 0.2 -9999 0 -0.5 40 40
IKK complex -0.038 0.12 -9999 0 -0.22 41 41
WIPF1 -0.002 0.099 -9999 0 -0.57 8 8
IL23-mediated signaling events

Figure S23.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S23.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.34 0.54 -9999 0 -1.3 50 50
IL23A -0.29 0.45 -9999 0 -1.1 43 43
NF kappa B1 p50/RelA/I kappa B alpha -0.32 0.4 -9999 0 -1 52 52
positive regulation of T cell mediated cytotoxicity -0.32 0.5 -9999 0 -1.1 54 54
ITGA3 -0.27 0.43 -9999 0 -1 44 44
IL17F -0.18 0.3 -9999 0 -0.67 46 46
IL12B -0.008 0.083 -9999 0 -0.48 7 7
STAT1 (dimer) -0.3 0.47 -9999 0 -1.1 52 52
CD4 -0.27 0.44 -9999 0 -1 43 43
IL23 -0.28 0.43 -9999 0 -1.1 43 43
IL23R -0.03 0.088 -9999 0 -10000 0 0
IL1B -0.31 0.49 -9999 0 -1.2 47 47
T-helper cell lineage commitment 0 0 -9999 0 -10000 0 0
IL24 -0.29 0.43 -9999 0 -0.98 52 52
TYK2 0.008 0.021 -9999 0 -10000 0 0
STAT4 -0.013 0.12 -9999 0 -0.57 13 13
STAT3 0.015 0 -9999 0 -10000 0 0
IL18RAP -0.017 0.13 -9999 0 -0.56 14 14
IL12RB1 -0.028 0.13 -9999 0 -0.52 18 18
PIK3CA 0.015 0 -9999 0 -10000 0 0
IL12Rbeta1/TYK2 -0.019 0.099 -9999 0 -0.37 18 18
IL23R/JAK2 -0.036 0.11 -9999 0 -10000 0 0
positive regulation of chronic inflammatory response -0.32 0.5 -9999 0 -1.1 54 54
natural killer cell activation 0.003 0.008 -9999 0 -10000 0 0
JAK2 0.012 0.045 -9999 0 -0.6 1 1
PIK3R1 0.015 0 -9999 0 -10000 0 0
NFKB1 0.014 0.004 -9999 0 -10000 0 0
RELA 0.014 0.004 -9999 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.27 0.41 -9999 0 -0.99 43 43
ALOX12B -0.28 0.43 -9999 0 -1 49 49
CXCL1 -0.33 0.51 -9999 0 -1.2 58 58
T cell proliferation -0.32 0.5 -9999 0 -1.1 54 54
NFKBIA 0.014 0.004 -9999 0 -10000 0 0
IL17A -0.12 0.25 -9999 0 -0.54 35 35
PI3K -0.32 0.41 -9999 0 -1 54 54
IFNG -0.016 0.033 -9999 0 -0.11 1 1
STAT3 (dimer) -0.31 0.38 -9999 0 -0.98 51 51
IL18R1 0.007 0.061 -9999 0 -0.56 3 3
IL23/IL23R/JAK2/TYK2/SOCS3 -0.18 0.31 -9999 0 -0.73 39 39
IL18/IL18R 0 0.11 -9999 0 -0.38 19 19
macrophage activation -0.017 0.017 -9999 0 -0.043 44 44
TNF -0.29 0.45 -9999 0 -1 50 50
STAT3/STAT4 -0.33 0.42 -9999 0 -1 55 55
STAT4 (dimer) -0.31 0.49 -9999 0 -1.1 53 53
IL18 0.003 0.078 -9999 0 -0.56 5 5
IL19 -0.28 0.43 -9999 0 -0.99 50 50
STAT5A (dimer) -0.3 0.47 -9999 0 -1.1 52 52
STAT1 0.009 0.053 -9999 0 -0.48 3 3
SOCS3 -0.046 0.18 -9999 0 -0.57 28 28
CXCL9 -0.32 0.45 -9999 0 -1 51 51
MPO -0.27 0.43 -9999 0 -0.99 48 48
positive regulation of humoral immune response -0.32 0.5 -9999 0 -1.1 54 54
IL23/IL23R/JAK2/TYK2 -0.33 0.53 -9999 0 -1.2 54 54
IL6 -0.61 0.68 -9999 0 -1.3 127 127
STAT5A 0.013 0.036 -9999 0 -0.57 1 1
IL2 0.005 0.012 -9999 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.003 0.008 -9999 0 -10000 0 0
CD3E -0.32 0.52 -9999 0 -1.2 56 56
keratinocyte proliferation -0.32 0.5 -9999 0 -1.1 54 54
NOS2 -0.29 0.46 -9999 0 -1.1 49 49
Ras signaling in the CD4+ TCR pathway

Figure S24.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S24.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.12 0.23 -9999 0 -0.41 85 85
MAP3K8 0.006 0.062 -9999 0 -0.57 3 3
FOS -0.089 0.18 -9999 0 -0.45 34 34
PRKCA 0.009 0.036 -9999 0 -0.57 1 1
PTPN7 -0.004 0.094 -9999 0 -0.54 8 8
HRAS 0.014 0.002 -9999 0 -10000 0 0
PRKCB -0.15 0.26 -9999 0 -0.57 75 75
NRAS 0.014 0.002 -9999 0 -10000 0 0
RAS family/GTP 0.021 0.023 -9999 0 -0.27 1 1
MAPK3 -0.047 0.13 -9999 0 -0.54 7 7
MAP2K1 -0.11 0.22 -9999 0 -0.45 75 75
ELK1 0.01 0.01 -9999 0 -10000 0 0
BRAF -0.1 0.21 -9999 0 -0.43 75 75
mol:GTP -0.001 0.003 -9999 0 -0.005 80 80
MAPK1 -0.047 0.13 -9999 0 -0.54 7 7
RAF1 -0.1 0.21 -9999 0 -0.43 75 75
KRAS 0.012 0.031 -9999 0 -0.49 1 1
Syndecan-1-mediated signaling events

Figure S25.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S25.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.015 0 -9999 0 -10000 0 0
CCL5 -0.018 0.13 -9999 0 -0.54 16 16
SDCBP 0.015 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.11 0.13 -9999 0 -0.33 40 40
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.099 0.12 -9999 0 -0.31 38 38
Syndecan-1/Syntenin -0.099 0.12 -9999 0 -0.31 38 38
MAPK3 -0.075 0.11 -9999 0 -0.38 10 10
HGF/MET -0.082 0.18 -9999 0 -0.4 66 66
TGFB1/TGF beta receptor Type II 0.015 0 -9999 0 -10000 0 0
BSG 0.015 0 -9999 0 -10000 0 0
keratinocyte migration -0.098 0.12 -9999 0 -0.3 38 38
Syndecan-1/RANTES -0.12 0.15 -9999 0 -0.35 48 48
Syndecan-1/CD147 -0.087 0.12 -9999 0 -0.36 15 15
Syndecan-1/Syntenin/PIP2 -0.095 0.12 -9999 0 -0.3 38 38
LAMA5 0.015 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.11 0.1 -9999 0 -0.29 38 38
MMP7 -0.1 0.22 -9999 0 -0.5 62 62
HGF -0.13 0.25 -9999 0 -0.56 66 66
Syndecan-1/CASK -0.11 0.12 -9999 0 -0.31 40 40
Syndecan-1/HGF/MET -0.16 0.18 -9999 0 -0.44 53 53
regulation of cell adhesion -0.065 0.11 -9999 0 -0.36 10 10
HPSE -0.036 0.15 -9999 0 -0.49 27 27
positive regulation of cell migration -0.11 0.13 -9999 0 -0.33 40 40
SDC1 -0.11 0.13 -9999 0 -0.33 40 40
Syndecan-1/Collagen -0.11 0.13 -9999 0 -0.33 40 40
PPIB 0.015 0 -9999 0 -10000 0 0
MET 0.015 0 -9999 0 -10000 0 0
PRKACA 0.015 0 -9999 0 -10000 0 0
MMP9 -0.13 0.23 -9999 0 -0.49 77 77
MAPK1 -0.075 0.11 -9999 0 -0.38 10 10
homophilic cell adhesion -0.11 0.13 -9999 0 -0.32 40 40
MMP1 -0.27 0.25 -9999 0 -0.48 154 154
Rapid glucocorticoid signaling

Figure S26.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S26.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma -0.11 0.16 -10000 0 -0.3 112 112
MAPK9 0.01 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.089 0.16 -10000 0 -0.35 72 72
GNB1/GNG2 0.016 0.039 -10000 0 -0.35 3 3
GNB1 0.015 0 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.01 0 -10000 0 -10000 0 0
Gs family/GTP -0.13 0.16 -10000 0 -0.32 112 112
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.035 0.041 0.084 112 -10000 0 112
GNAL -0.23 0.29 -10000 0 -0.57 112 112
GNG2 0.009 0.061 -10000 0 -0.57 3 3
CRH -0.13 0.22 -10000 0 -0.49 72 72
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.006 0.038 -10000 0 -0.35 3 3
MAPK11 0.01 0 -10000 0 -10000 0 0
Integrins in angiogenesis

Figure S27.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S27.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.022 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.13 0.23 -9999 0 -0.42 93 93
PTK2 -0.099 0.23 -9999 0 -0.54 44 44
IGF1R 0.011 0.05 -9999 0 -0.57 2 2
PI4KB 0.015 0 -9999 0 -10000 0 0
MFGE8 0.013 0.036 -9999 0 -0.57 1 1
SRC 0.015 0 -9999 0 -10000 0 0
CDKN1B -0.13 0.28 -9999 0 -0.73 44 44
VEGFA 0.015 0 -9999 0 -10000 0 0
ILK -0.13 0.28 -9999 0 -0.73 44 44
ROCK1 0.015 0 -9999 0 -10000 0 0
AKT1 -0.12 0.27 -9999 0 -0.68 44 44
PTK2B 0.008 0.1 -9999 0 -0.56 1 1
alphaV/beta3 Integrin/JAM-A -0.14 0.26 -9999 0 -0.63 46 46
CBL 0.015 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.014 0.12 -9999 0 -0.35 30 30
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.12 0.18 -9999 0 -0.31 124 124
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.017 0.13 -9999 0 -0.42 12 12
alphaV/beta3 Integrin/Syndecan-1 -0.014 0.12 -9999 0 -0.35 32 32
PI4KA 0.015 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.25 0.28 -9999 0 -0.61 88 88
PI4 Kinase 0.022 0 -9999 0 -10000 0 0
PIK3CA 0.015 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.13 0.17 -9999 0 -0.29 134 134
RPS6KB1 -0.21 0.28 -9999 0 -0.56 88 88
TLN1 0.015 0 -9999 0 -10000 0 0
MAPK3 -0.27 0.4 -9999 0 -0.78 94 94
GPR124 -0.039 0.17 -9999 0 -0.57 25 25
MAPK1 -0.27 0.4 -9999 0 -0.78 94 94
PXN 0.015 0 -9999 0 -10000 0 0
PIK3R1 0.015 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.12 0.21 -9999 0 -0.38 94 94
cell adhesion -0.029 0.11 -9999 0 -0.34 29 29
ANGPTL3 0.009 0.031 -9999 0 -0.48 1 1
VEGFR2 homodimer/VEGFA homodimer/Src 0.031 0 -9999 0 -10000 0 0
IGF-1R heterotetramer 0.011 0.05 -9999 0 -0.56 2 2
Rac1/GDP 0.011 0 -9999 0 -10000 0 0
TGFBR2 0.011 0.05 -9999 0 -0.57 2 2
ITGB3 -0.048 0.18 -9999 0 -0.57 29 29
IGF1 -0.25 0.29 -9999 0 -0.57 121 121
RAC1 0.015 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.042 0.18 -9999 0 -0.44 41 41
apoptosis 0.013 0.035 -9999 0 -0.56 1 1
CD47 0.015 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.01 0.12 -9999 0 -0.35 29 29
VCL 0.013 0.036 -9999 0 -0.57 1 1
alphaV/beta3 Integrin/Del1 -0.053 0.2 -9999 0 -0.46 45 45
CSF1 -0.011 0.12 -9999 0 -0.57 12 12
PIK3C2A -0.13 0.28 -9999 0 -0.73 44 44
PI4 Kinase/Pyk2 -0.14 0.2 -9999 0 -0.53 47 47
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.001 0.11 -9999 0 -0.31 29 29
FAK1/Vinculin -0.07 0.18 -9999 0 -0.41 45 45
alphaV beta3/Integrin/ppsTEM5 -0.042 0.18 -9999 0 -0.45 41 41
RHOA 0.015 0 -9999 0 -10000 0 0
VTN -0.083 0.22 -9999 0 -0.56 45 45
BCAR1 0.015 0 -9999 0 -10000 0 0
FGF2 -0.17 0.27 -9999 0 -0.57 87 87
F11R -0.12 0.2 -9999 0 -0.41 88 88
alphaV/beta3 Integrin/Lactadherin -0.012 0.12 -9999 0 -0.36 29 29
alphaV/beta3 Integrin/TGFBR2 -0.013 0.13 -9999 0 -0.36 30 30
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.023 0.072 -9999 0 -0.3 13 13
HSP90AA1 0.015 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.008 0.11 -9999 0 -0.32 29 29
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.032 0.15 -9999 0 -0.51 24 24
alphaV/beta3 Integrin/Pyk2 0.009 0.1 -9999 0 -0.57 1 1
SDC1 0.009 0.061 -9999 0 -0.57 3 3
VAV3 0.021 0.079 -9999 0 -0.27 15 15
PTPN11 0.015 0 -9999 0 -10000 0 0
IRS1 0.002 0.086 -9999 0 -0.57 6 6
FAK1/Paxillin -0.069 0.18 -9999 0 -0.41 44 44
cell migration -0.055 0.17 -9999 0 -0.4 32 32
ITGAV 0.013 0.036 -9999 0 -0.57 1 1
PI3K -0.15 0.22 -9999 0 -0.57 46 46
SPP1 -0.18 0.24 -9999 0 -0.48 107 107
KDR 0.015 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.013 0.035 -9999 0 -0.56 1 1
COL4A3 -0.15 0.26 -9999 0 -0.56 77 77
angiogenesis -0.26 0.39 -9999 0 -0.76 95 95
Rac1/GTP 0.028 0.073 -9999 0 -10000 0 0
EDIL3 -0.057 0.19 -9999 0 -0.57 33 33
cell proliferation -0.013 0.12 -9999 0 -0.36 30 30
Glypican 1 network

Figure S28.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S28.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer -0.17 0.27 -9999 0 -0.5 100 100
fibroblast growth factor receptor signaling pathway -0.17 0.27 -9999 0 -0.5 100 100
LAMA1 -0.083 0.2 -9999 0 -0.5 51 51
PRNP 0.004 0.079 -9999 0 -0.57 5 5
GPC1/SLIT2 -0.17 0.21 -9999 0 -0.41 122 122
SMAD2 0.035 0.029 -9999 0 -0.3 2 2
GPC1/PrPc/Cu2+ 0.014 0.05 -9999 0 -0.35 5 5
GPC1/Laminin alpha1 -0.049 0.15 -9999 0 -0.35 51 51
TDGF1 0.007 0.031 -9999 0 -0.48 1 1
CRIPTO/GPC1 0.016 0.022 -9999 0 -0.34 1 1
APP/GPC1 0.019 0.037 -9999 0 -0.41 2 2
mol:NO 0 0 -9999 0 -10000 0 0
YES1 0.026 0.019 -9999 0 -10000 0 0
FLT1 0.015 0 -9999 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.028 0.032 -9999 0 -0.34 2 2
SERPINC1 -0.015 0.11 -9999 0 -0.48 15 15
FYN 0.022 0.043 -9999 0 -0.34 3 3
FGR 0.024 0.029 -9999 0 -0.3 2 2
positive regulation of MAPKKK cascade 0.02 0.076 -9999 0 -0.35 3 3
SLIT2 -0.25 0.29 -9999 0 -0.57 122 122
GPC1/NRG -0.075 0.18 -9999 0 -0.39 63 63
NRG1 -0.12 0.24 -9999 0 -0.55 63 63
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.031 0 -9999 0 -10000 0 0
LYN 0.026 0.019 -9999 0 -10000 0 0
mol:Spermine 0.013 0 -9999 0 -10000 0 0
cell growth -0.17 0.27 -9999 0 -0.5 100 100
BMP signaling pathway -0.015 0 -9999 0 -10000 0 0
SRC 0.026 0.019 -9999 0 -0.27 1 1
TGFBR1 0.015 0 -9999 0 -10000 0 0
mol:Cu2+ 0 0 -9999 0 -10000 0 0
PLA2G2A -0.26 0.29 -9999 0 -0.57 124 124
GPC1 0.015 0 -9999 0 -10000 0 0
TGFBR1 (dimer) 0.015 0 -9999 0 -10000 0 0
VEGFA 0.015 0 -9999 0 -10000 0 0
BLK -0.019 0.12 -9999 0 -0.32 34 34
HCK 0.01 0.075 -9999 0 -0.32 13 13
FGF2 -0.17 0.27 -9999 0 -0.57 87 87
FGFR1 -0.12 0.25 -9999 0 -0.57 63 63
VEGFR1 homodimer 0.015 0 -9999 0 -10000 0 0
TGFBR2 0.011 0.05 -9999 0 -0.57 2 2
cell death 0.019 0.037 -9999 0 -0.4 2 2
ATIII/GPC1 0.001 0.082 -9999 0 -0.34 15 15
PLA2G2A/GPC1 -0.18 0.21 -9999 0 -0.4 124 124
LCK 0.019 0.052 -9999 0 -0.32 6 6
neuron differentiation -0.075 0.18 -9999 0 -0.39 63 63
PrPc/Cu2+ 0.003 0.058 -9999 0 -0.42 5 5
APP 0.011 0.05 -9999 0 -0.57 2 2
TGFBR2 (dimer) 0.011 0.05 -9999 0 -0.56 2 2
PDGFR-alpha signaling pathway

Figure S29.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S29.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.082 0.21 -9999 0 -0.59 40 40
PDGF/PDGFRA/CRKL -0.048 0.16 -9999 0 -0.42 41 41
positive regulation of JUN kinase activity -0.016 0.12 -9999 0 -0.29 40 40
CRKL 0.011 0.043 -9999 0 -0.48 2 2
PDGF/PDGFRA/Caveolin-3 -0.056 0.15 -9999 0 -0.42 41 41
AP1 -0.32 0.46 -9999 0 -1 80 80
mol:IP3 -0.055 0.16 -9999 0 -0.43 40 40
PLCG1 -0.055 0.16 -9999 0 -0.44 40 40
PDGF/PDGFRA/alphaV Integrin -0.047 0.16 -9999 0 -0.42 40 40
RAPGEF1 0.015 0 -9999 0 -10000 0 0
CRK 0.015 0 -9999 0 -10000 0 0
mol:Ca2+ -0.055 0.16 -9999 0 -0.43 40 40
CAV3 0.002 0.031 -9999 0 -0.48 1 1
CAV1 -0.011 0.12 -9999 0 -0.57 12 12
SHC/Grb2/SOS1 -0.015 0.12 -9999 0 -0.3 40 40
PDGF/PDGFRA/Shf -0.053 0.17 -9999 0 -0.44 42 42
FOS -0.29 0.48 -9999 0 -1 80 80
JUN -0.032 0.078 -9999 0 -0.47 7 7
oligodendrocyte development -0.047 0.16 -9999 0 -0.42 40 40
GRB2 0.015 0 -9999 0 -10000 0 0
PIK3R1 0.015 0 -9999 0 -10000 0 0
mol:DAG -0.055 0.16 -9999 0 -0.43 40 40
PDGF/PDGFRA -0.082 0.21 -9999 0 -0.58 40 40
actin cytoskeleton reorganization -0.046 0.15 -9999 0 -0.41 40 40
SRF 0.032 0.012 -9999 0 -10000 0 0
SHC1 0.013 0.03 -9999 0 -0.48 1 1
PI3K -0.028 0.13 -9999 0 -0.34 40 40
PDGF/PDGFRA/Crk/C3G -0.028 0.13 -9999 0 -0.34 40 40
JAK1 -0.044 0.15 -9999 0 -0.41 40 40
ELK1/SRF -0.014 0.13 -9999 0 -0.31 40 40
SHB 0.015 0 -9999 0 -10000 0 0
SHF 0.004 0.079 -9999 0 -0.57 5 5
CSNK2A1 0.021 0.028 -9999 0 -10000 0 0
GO:0007205 -0.059 0.17 -9999 0 -0.46 40 40
SOS1 0.015 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.016 0.12 -9999 0 -0.29 40 40
PDGF/PDGFRA/SHB -0.046 0.15 -9999 0 -0.41 40 40
PDGF/PDGFRA/Caveolin-1 -0.064 0.18 -9999 0 -0.45 47 47
ITGAV 0.013 0.036 -9999 0 -0.57 1 1
ELK1 -0.053 0.16 -9999 0 -0.41 40 40
PIK3CA 0.015 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk -0.046 0.15 -9999 0 -0.41 40 40
JAK-STAT cascade -0.043 0.15 -9999 0 -0.41 40 40
cell proliferation -0.053 0.17 -9999 0 -0.43 42 42
amb2 Integrin signaling

Figure S30.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S30.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.081 0.17 -9999 0 -0.44 42 42
alphaM/beta2 Integrin/GPIbA -0.057 0.13 -9999 0 -0.4 29 29
alphaM/beta2 Integrin/proMMP-9 -0.13 0.18 -9999 0 -0.36 88 88
PLAUR 0.015 0 -9999 0 -10000 0 0
HMGB1 -0.004 0.023 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.049 0.12 -9999 0 -0.41 23 23
AGER -0.014 0.073 -9999 0 -0.51 5 5
RAP1A 0.015 0 -9999 0 -10000 0 0
SELPLG 0.003 0.082 -9999 0 -0.54 6 6
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.11 0.14 -9999 0 -0.49 20 20
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.13 0.23 -9999 0 -0.49 77 77
CYR61 -0.15 0.26 -9999 0 -0.57 76 76
TLN1 0.015 0 -9999 0 -10000 0 0
Rap1/GTP -0.057 0.12 -9999 0 -0.45 18 18
RHOA 0.015 0 -9999 0 -10000 0 0
P-selectin oligomer -0.1 0.23 -9999 0 -0.56 54 54
MYH2 -0.053 0.14 -9999 0 -0.41 22 22
MST1R -0.016 0.13 -9999 0 -0.53 15 15
leukocyte activation during inflammatory response -0.12 0.17 -9999 0 -0.36 81 81
APOB -0.081 0.21 -9999 0 -0.56 43 43
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.039 0.17 -9999 0 -0.57 25 25
JAM3 -0.015 0.13 -9999 0 -0.57 14 14
GP1BA 0 0.082 -9999 0 -0.5 7 7
alphaM/beta2 Integrin/CTGF -0.12 0.2 -9999 0 -0.44 67 67
alphaM/beta2 Integrin -0.053 0.16 -9999 0 -0.5 20 20
JAM3 homodimer -0.015 0.13 -9999 0 -0.56 14 14
ICAM2 0.013 0.036 -9999 0 -0.57 1 1
ICAM1 0.004 0.074 -9999 0 -0.48 6 6
phagocytosis triggered by activation of immune response cell surface activating receptor -0.052 0.16 -9999 0 -0.5 20 20
cell adhesion -0.057 0.13 -9999 0 -0.39 29 29
NFKB1 -0.14 0.22 -9999 0 -0.58 19 19
THY1 0.011 0.043 -9999 0 -0.48 2 2
RhoA/GDP 0.011 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.085 0.17 -9999 0 -0.37 69 69
alphaM/beta2 Integrin/LRP/tPA -0.038 0.16 -9999 0 -0.46 27 27
IL6 -0.33 0.41 -9999 0 -0.76 125 125
ITGB2 -0.028 0.11 -9999 0 -0.52 12 12
elevation of cytosolic calcium ion concentration -0.072 0.13 -9999 0 -0.36 33 33
alphaM/beta2 Integrin/JAM2/JAM3 -0.12 0.22 -9999 0 -0.42 80 80
JAM2 -0.13 0.25 -9999 0 -0.57 67 67
alphaM/beta2 Integrin/ICAM1 -0.063 0.14 -9999 0 -0.48 18 18
alphaM/beta2 Integrin/uPA/Plg -0.076 0.14 -9999 0 -0.36 35 35
RhoA/GTP -0.043 0.14 -9999 0 -0.43 20 20
positive regulation of phagocytosis -0.068 0.16 -9999 0 -0.49 25 25
Ron/MSP -0.016 0.12 -9999 0 -0.39 25 25
alphaM/beta2 Integrin/uPAR/uPA -0.056 0.14 -9999 0 -0.36 33 33
alphaM/beta2 Integrin/uPAR -0.049 0.12 -9999 0 -0.41 23 23
PLAU -0.052 0.17 -9999 0 -0.48 36 36
PLAT -0.015 0.13 -9999 0 -0.55 14 14
actin filament polymerization -0.05 0.14 -9999 0 -0.39 22 22
MST1 -0.008 0.1 -9999 0 -0.49 12 12
alphaM/beta2 Integrin/lipoprotein(a) -0.12 0.18 -9999 0 -0.36 81 81
TNF -0.13 0.2 -9999 0 -0.55 18 18
RAP1B 0.015 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.087 0.14 -9999 0 -0.34 58 58
fibrinolysis -0.079 0.13 -9999 0 -0.36 35 35
HCK -0.01 0.12 -9999 0 -0.55 12 12
dendritic cell antigen processing and presentation -0.052 0.16 -9999 0 -0.5 20 20
VTN -0.083 0.22 -9999 0 -0.56 45 45
alphaM/beta2 Integrin/CYR61 -0.15 0.22 -9999 0 -0.44 85 85
LPA -0.058 0.18 -9999 0 -0.56 32 32
LRP1 0.009 0.061 -9999 0 -0.57 3 3
cell migration -0.13 0.21 -9999 0 -0.44 58 58
FN1 -0.032 0.15 -9999 0 -0.51 24 24
alphaM/beta2 Integrin/Thy1 -0.051 0.12 -9999 0 -0.4 25 25
MPO 0.011 0.031 -9999 0 -0.48 1 1
KNG1 0 0 -9999 0 -10000 0 0
RAP1/GDP 0.021 0 -9999 0 -10000 0 0
ROCK1 -0.032 0.14 -9999 0 -0.42 18 18
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.001 0.042 -9999 0 -0.48 2 2
CTGF -0.1 0.23 -9999 0 -0.57 54 54
alphaM/beta2 Integrin/Hck -0.063 0.16 -9999 0 -0.49 27 27
ITGAM -0.039 0.14 -9999 0 -0.58 16 16
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.092 0.2 -9999 0 -0.39 68 68
HP -0.042 0.16 -9999 0 -0.49 29 29
leukocyte adhesion -0.16 0.2 -9999 0 -0.48 64 64
SELP -0.1 0.23 -9999 0 -0.57 54 54
BMP receptor signaling

Figure S31.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S31.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.13 0.21 -9999 0 -0.55 29 29
SMAD6-7/SMURF1 0.026 0.041 -9999 0 -0.3 4 4
NOG -0.028 0.14 -9999 0 -0.48 22 22
SMAD9 -0.15 0.25 -9999 0 -0.56 68 68
SMAD4 0.015 0 -9999 0 -10000 0 0
SMAD5 -0.035 0.11 -9999 0 -0.33 9 9
BMP7/USAG1 -0.26 0.26 -9999 0 -0.47 155 155
SMAD5/SKI -0.025 0.1 -9999 0 -0.36 5 5
SMAD1 0.044 0.021 -9999 0 -10000 0 0
BMP2 -0.05 0.18 -9999 0 -0.57 30 30
SMAD1/SMAD1/SMAD4 -0.003 0.021 -9999 0 -10000 0 0
BMPR1A 0.015 0 -9999 0 -10000 0 0
BMPR1B -0.071 0.19 -9999 0 -0.49 45 45
BMPR1A-1B/BAMBI -0.052 0.16 -9999 0 -0.34 59 59
AHSG -0.035 0.13 -9999 0 -0.48 22 22
CER1 0.004 0.007 -9999 0 -10000 0 0
BMP2-4/CER1 -0.034 0.13 -9999 0 -0.34 42 42
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.067 0.15 -9999 0 -0.36 26 26
BMP2-4 (homodimer) -0.044 0.15 -9999 0 -0.4 42 42
RGMB 0.015 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.01 0.11 -9999 0 -0.3 4 4
RGMA -0.16 0.26 -9999 0 -0.57 78 78
SMURF1 0.015 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.068 0.13 -9999 0 -0.34 28 28
BMP2-4/USAG1 -0.15 0.22 -9999 0 -0.39 114 114
SMAD6/SMURF1/SMAD5 -0.025 0.1 -9999 0 -0.36 5 5
SOSTDC1 -0.18 0.27 -9999 0 -0.56 91 91
BMP7/BMPR2/BMPR1A-1B -0.12 0.2 -9999 0 -0.35 97 97
SKI 0.015 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.013 0.03 -9999 0 -0.48 1 1
HFE2 0.004 0.031 -9999 0 -0.48 1 1
ZFYVE16 0.015 0 -9999 0 -10000 0 0
MAP3K7 0.015 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.061 0.18 -9999 0 -0.37 61 61
SMAD5/SMAD5/SMAD4 -0.025 0.1 -9999 0 -0.36 5 5
MAPK1 0.015 0 -9999 0 -10000 0 0
TAK1/TAB family -0.071 0.094 -9999 0 -0.35 14 14
BMP7 (homodimer) -0.19 0.28 -9999 0 -0.56 93 93
NUP214 0.015 0 -9999 0 -10000 0 0
BMP6/FETUA -0.015 0.099 -9999 0 -0.34 23 23
SMAD1/SKI 0.051 0.019 -9999 0 -10000 0 0
SMAD6 0.009 0.056 -9999 0 -0.51 3 3
CTDSP2 0.015 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.057 0.16 -9999 0 -0.34 59 59
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.15 0.25 -9999 0 -0.53 83 83
BMPR2 (homodimer) 0.015 0 -9999 0 -10000 0 0
GADD34/PP1CA 0.031 0 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.04 0.14 -9999 0 -0.34 45 45
CHRDL1 -0.31 0.29 -9999 0 -0.57 150 150
ENDOFIN/SMAD1 0.051 0.019 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 0.001 0.026 -9999 0 -10000 0 0
SMAD6/SMURF1 0.015 0 -9999 0 -10000 0 0
BAMBI -0.034 0.16 -9999 0 -0.56 23 23
SMURF2 0.015 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.23 0.22 -9999 0 -0.38 168 168
BMP2-4/GREM1 -0.13 0.18 -9999 0 -0.33 121 121
SMAD7 0.013 0.036 -9999 0 -0.57 1 1
SMAD8A/SMAD8A/SMAD4 -0.13 0.24 -9999 0 -0.52 68 68
SMAD1/SMAD6 0.051 0.019 -9999 0 -10000 0 0
TAK1/SMAD6 0.022 0 -9999 0 -10000 0 0
BMP7 -0.19 0.28 -9999 0 -0.57 93 93
BMP6 0.013 0.03 -9999 0 -0.48 1 1
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.061 0.13 -9999 0 -0.32 29 29
PPM1A 0.015 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.051 0.019 -9999 0 -10000 0 0
SMAD7/SMURF1 0.021 0.026 -9999 0 -0.41 1 1
CTDSPL 0.015 0 -9999 0 -10000 0 0
PPP1CA 0.015 0 -9999 0 -10000 0 0
XIAP 0.013 0.03 -9999 0 -0.48 1 1
CTDSP1 0.015 0 -9999 0 -10000 0 0
PPP1R15A 0.015 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.097 0.17 -9999 0 -0.43 34 34
CHRD -0.041 0.17 -9999 0 -0.56 26 26
BMPR2 0.015 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.083 0.15 -9999 0 -0.39 28 28
BMP4 -0.01 0.12 -9999 0 -0.55 12 12
FST -0.03 0.15 -9999 0 -0.54 22 22
BMP2-4/NOG -0.052 0.17 -9999 0 -0.37 54 54
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.11 0.19 -9999 0 -0.5 23 23
Glucocorticoid receptor regulatory network

Figure S32.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S32.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.014 0.058 -10000 0 -10000 0 0
SMARCC2 0.014 0.016 -10000 0 -10000 0 0
SMARCC1 0.014 0.016 -10000 0 -10000 0 0
TBX21 -0.072 0.19 -10000 0 -0.68 17 17
SUMO2 0.011 0.007 -10000 0 -10000 0 0
STAT1 (dimer) 0.019 0.052 -10000 0 -0.47 3 3
FKBP4 0.015 0 -10000 0 -10000 0 0
FKBP5 -0.015 0.13 -10000 0 -0.57 14 14
GR alpha/HSP90/FKBP51/HSP90 0.08 0.12 0.26 16 -0.3 1 17
PRL -0.062 0.12 -10000 0 -0.47 6 6
cortisol/GR alpha (dimer)/TIF2 0.21 0.22 0.46 78 -0.41 2 80
RELA -0.097 0.12 -10000 0 -0.27 26 26
FGG 0.16 0.2 0.43 39 -0.51 2 41
GR beta/TIF2 0.08 0.14 0.28 21 -0.38 12 33
IFNG -0.3 0.24 -10000 0 -0.67 47 47
apoptosis -0.062 0.18 0.42 4 -0.55 7 11
CREB1 0.013 0.031 -10000 0 -10000 0 0
histone acetylation -0.012 0.14 0.49 1 -0.34 21 22
BGLAP -0.041 0.1 -10000 0 -0.5 1 1
GR/PKAc 0.098 0.087 0.27 11 -10000 0 11
NF kappa B1 p50/RelA -0.18 0.23 -10000 0 -0.45 89 89
SMARCD1 0.014 0.016 -10000 0 -10000 0 0
MDM2 0.089 0.084 0.21 36 -0.22 2 38
GATA3 -0.022 0.15 -10000 0 -0.56 20 20
AKT1 0.002 0.006 -10000 0 -10000 0 0
CSF2 -0.076 0.12 -10000 0 -0.5 2 2
GSK3B 0.011 0.007 -10000 0 -10000 0 0
NR1I3 -0.02 0.17 0.46 1 -0.51 2 3
CSN2 0.16 0.14 0.36 33 -10000 0 33
BRG1/BAF155/BAF170/BAF60A 0.038 0.054 -10000 0 -0.3 3 3
NFATC1 -0.012 0.12 -10000 0 -0.56 13 13
POU2F1 0.017 0.011 -10000 0 -10000 0 0
CDKN1A 0.034 0.093 -10000 0 -1.4 1 1
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.003 0.006 -10000 0 -10000 0 0
SFN -0.036 0.15 -10000 0 -0.49 27 27
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.07 0.12 0.28 9 -10000 0 9
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.15 0.38 0.44 1 -0.83 62 63
JUN -0.16 0.16 -10000 0 -0.45 36 36
IL4 -0.085 0.14 -10000 0 -0.55 12 12
CDK5R1 -0.016 0.12 -10000 0 -0.48 16 16
PRKACA 0.015 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.23 0.27 -10000 0 -0.55 84 84
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.089 0.11 0.27 11 -10000 0 11
cortisol/GR alpha (monomer) 0.26 0.23 0.53 82 -10000 0 82
NCOA2 -0.02 0.14 -10000 0 -0.57 16 16
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.22 0.27 -10000 0 -0.62 80 80
AP-1/NFAT1-c-4 -0.38 0.31 -10000 0 -0.68 111 111
AFP -0.13 0.14 -10000 0 -0.54 6 6
SUV420H1 0.015 0 -10000 0 -10000 0 0
IRF1 0.16 0.12 0.39 15 -10000 0 15
TP53 0.038 0.032 -10000 0 -0.49 1 1
PPP5C 0.015 0 -10000 0 -10000 0 0
KRT17 -0.35 0.38 -10000 0 -0.84 69 69
KRT14 -0.22 0.23 -10000 0 -0.55 46 46
TBP 0.025 0.013 -10000 0 -10000 0 0
CREBBP 0.067 0.084 0.3 3 -0.25 3 6
HDAC1 0.013 0.007 -10000 0 -10000 0 0
HDAC2 0.019 0.012 -10000 0 -10000 0 0
AP-1 -0.38 0.32 -10000 0 -0.69 111 111
MAPK14 0.012 0.007 -10000 0 -10000 0 0
MAPK10 -0.043 0.17 -10000 0 -0.57 25 25
MAPK11 0.011 0.007 -10000 0 -10000 0 0
KRT5 -0.55 0.54 -10000 0 -1.1 111 111
interleukin-1 receptor activity 0.003 0.012 -10000 0 -10000 0 0
NCOA1 0.019 0.003 -10000 0 -10000 0 0
STAT1 0.019 0.052 -10000 0 -0.47 3 3
CGA -0.069 0.13 -10000 0 -0.55 3 3
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.11 0.14 0.33 43 -0.47 2 45
MAPK3 0.011 0.007 -10000 0 -10000 0 0
MAPK1 0.012 0.007 -10000 0 -10000 0 0
ICAM1 -0.24 0.24 -10000 0 -0.54 71 71
NFKB1 -0.097 0.12 -10000 0 -0.29 11 11
MAPK8 -0.13 0.14 -10000 0 -0.38 36 36
MAPK9 0.012 0.007 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.073 0.18 0.42 4 -0.58 7 11
BAX 0.038 0.032 -10000 0 -10000 0 0
POMC -0.3 0.32 -10000 0 -0.58 101 101
EP300 0.067 0.084 0.3 3 -0.25 2 5
cortisol/GR alpha (dimer)/p53 0.26 0.2 0.48 83 -10000 0 83
proteasomal ubiquitin-dependent protein catabolic process 0.061 0.067 0.2 7 -0.21 1 8
SGK1 0.082 0.28 0.4 1 -1.3 10 11
IL13 -0.23 0.22 -10000 0 -0.69 28 28
IL6 -0.6 0.6 -10000 0 -1.2 129 129
PRKACG 0.002 0.006 -10000 0 -10000 0 0
IL5 -0.21 0.18 -10000 0 -0.62 22 22
IL2 -0.27 0.21 -10000 0 -0.6 47 47
CDK5 0.014 0.003 -10000 0 -10000 0 0
PRKACB 0.011 0.05 -10000 0 -0.57 2 2
HSP90AA1 0.015 0 -10000 0 -10000 0 0
IL8 -0.35 0.45 -10000 0 -1 63 63
CDK5R1/CDK5 -0.005 0.085 -10000 0 -0.34 16 16
NF kappa B1 p50/RelA/PKAc -0.11 0.18 -10000 0 -0.38 32 32
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.24 0.18 0.44 80 -10000 0 80
SMARCA4 0.014 0.016 -10000 0 -10000 0 0
chromatin remodeling 0.15 0.14 0.33 51 -0.42 4 55
NF kappa B1 p50/RelA/Cbp -0.076 0.23 0.39 1 -0.43 38 39
JUN (dimer) -0.16 0.16 -10000 0 -0.45 36 36
YWHAH 0.015 0 -10000 0 -10000 0 0
VIPR1 -0.078 0.2 -10000 0 -0.64 23 23
NR3C1 0.15 0.14 0.36 44 -0.45 2 46
NR4A1 -0.31 0.3 -10000 0 -0.57 148 148
TIF2/SUV420H1 -0.003 0.1 -10000 0 -0.41 16 16
MAPKKK cascade -0.062 0.18 0.42 4 -0.55 7 11
cortisol/GR alpha (dimer)/Src-1 0.24 0.2 0.47 80 -10000 0 80
PBX1 -0.014 0.13 -10000 0 -0.56 14 14
POU1F1 0.004 0.033 -10000 0 -0.48 1 1
SELE -0.53 0.57 -10000 0 -1.1 121 121
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.15 0.14 0.33 48 -0.42 4 52
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.24 0.18 0.44 80 -10000 0 80
mol:cortisol 0.14 0.13 0.29 90 -10000 0 90
MMP1 -0.24 0.16 -10000 0 -0.43 75 75
TCR signaling in naïve CD8+ T cells

Figure S33.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S33.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GRB2/SOS1/SHC -0.091 0.2 -10000 0 -0.55 40 40
FYN -0.076 0.32 -10000 0 -0.74 45 45
LAT/GRAP2/SLP76 -0.1 0.24 -10000 0 -0.6 45 45
IKBKB 0.015 0 -10000 0 -10000 0 0
AKT1 -0.028 0.2 -10000 0 -0.46 42 42
B2M 0.015 0.005 -10000 0 -10000 0 0
IKBKG -0.022 0.044 -10000 0 -0.13 18 18
MAP3K8 0.009 0.061 -10000 0 -0.57 3 3
mol:Ca2+ -0.023 0.038 -10000 0 -0.11 29 29
integrin-mediated signaling pathway 0.018 0.031 -10000 0 -0.34 2 2
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.067 0.3 -10000 0 -0.69 44 44
TRPV6 -0.11 0.22 -10000 0 -0.54 56 56
CD28 -0.013 0.12 -10000 0 -0.56 13 13
SHC1 -0.067 0.3 -10000 0 -0.68 45 45
receptor internalization -0.078 0.31 -10000 0 -0.7 45 45
PRF1 -0.079 0.33 -10000 0 -0.91 28 28
KRAS 0.013 0.03 -10000 0 -0.48 1 1
GRB2 0.015 0 -10000 0 -10000 0 0
COT/AKT1 -0.012 0.16 -10000 0 -0.37 40 40
LAT -0.067 0.3 -10000 0 -0.67 45 45
EntrezGene:6955 0 0.004 -10000 0 -10000 0 0
CD3D -0.043 0.18 -10000 0 -0.57 27 27
CD3E -0.046 0.18 -10000 0 -0.58 28 28
CD3G -0.049 0.18 -10000 0 -0.57 29 29
RASGRP2 -0.044 0.083 -10000 0 -0.17 76 76
RASGRP1 -0.024 0.21 -10000 0 -0.47 41 41
HLA-A 0.012 0.037 -10000 0 -0.58 1 1
RASSF5 0.011 0.05 -10000 0 -0.57 2 2
RAP1A/GTP/RAPL 0.018 0.032 -10000 0 -0.35 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.005 0.069 -10000 0 -0.13 41 41
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.041 0.077 -10000 0 -0.22 33 33
PRKCA -0.041 0.11 -10000 0 -0.28 40 40
GRAP2 -0.059 0.19 -10000 0 -0.57 34 34
mol:IP3 -0.043 0.2 0.22 48 -0.45 41 89
EntrezGene:6957 0 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.081 0.31 -10000 0 -0.72 40 40
ORAI1 0.065 0.12 0.3 56 -0.35 1 57
CSK -0.069 0.3 -10000 0 -0.69 45 45
B7 family/CD28 -0.14 0.27 -10000 0 -0.65 48 48
CHUK 0.015 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.093 0.35 -10000 0 -0.8 46 46
PTPN6 -0.073 0.3 -10000 0 -0.69 45 45
VAV1 -0.076 0.32 -10000 0 -0.71 46 46
Monovalent TCR/CD3 -0.071 0.25 -10000 0 -0.52 50 50
CBL 0.015 0 -10000 0 -10000 0 0
LCK -0.081 0.33 -10000 0 -0.75 45 45
PAG1 -0.069 0.3 -10000 0 -0.7 43 43
RAP1A 0.015 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.093 0.35 -10000 0 -0.79 45 45
CD80 -0.042 0.16 -10000 0 -0.48 30 30
CD86 0.008 0.062 -10000 0 -0.57 3 3
PDK1/CARD11/BCL10/MALT1 -0.05 0.094 -10000 0 -0.26 37 37
HRAS 0.015 0 -10000 0 -10000 0 0
GO:0035030 -0.062 0.24 -10000 0 -0.53 48 48
CD8A -0.043 0.18 -10000 0 -0.57 27 27
CD8B -0.037 0.17 -10000 0 -0.56 24 24
PTPRC -0.063 0.2 -10000 0 -0.57 36 36
PDK1/PKC theta -0.041 0.25 -10000 0 -0.57 44 44
CSK/PAG1 -0.061 0.29 -10000 0 -0.7 40 40
SOS1 0.015 0 -10000 0 -10000 0 0
peptide-MHC class I 0.019 0.029 -10000 0 -0.42 1 1
GRAP2/SLP76 -0.12 0.29 -10000 0 -0.7 46 46
STIM1 0.035 0.061 -10000 0 -10000 0 0
RAS family/GTP 0.022 0.086 -10000 0 -0.17 32 32
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.088 0.34 -10000 0 -0.78 44 44
mol:DAG -0.059 0.16 -10000 0 -0.4 42 42
RAP1A/GDP 0.004 0.03 -10000 0 -0.063 7 7
PLCG1 0.015 0 -10000 0 -10000 0 0
CD247 0.002 0.085 -10000 0 -0.56 6 6
cytotoxic T cell degranulation -0.072 0.31 -10000 0 -0.77 33 33
RAP1A/GTP -0.019 0.027 -10000 0 -0.068 27 27
mol:PI-3-4-5-P3 -0.045 0.24 -10000 0 -0.55 44 44
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.066 0.26 0.24 46 -0.6 42 88
NRAS 0.015 0 -10000 0 -10000 0 0
ZAP70 -0.009 0.12 -10000 0 -0.57 11 11
GRB2/SOS1 0.022 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.1 0.23 -10000 0 -0.59 44 44
MALT1 0.015 0 -10000 0 -10000 0 0
TRAF6 0.015 0 -10000 0 -10000 0 0
CD8 heterodimer -0.054 0.2 -10000 0 -0.54 37 37
CARD11 -0.002 0.096 -10000 0 -0.55 8 8
PRKCB -0.085 0.15 -10000 0 -0.35 54 54
PRKCE -0.04 0.11 -10000 0 -0.28 40 40
PRKCQ -0.062 0.29 -10000 0 -0.67 44 44
LCP2 0.013 0.036 -10000 0 -0.57 1 1
BCL10 0.015 0 -10000 0 -10000 0 0
regulation of survival gene product expression -0.018 0.17 -10000 0 -0.39 42 42
IKK complex 0.014 0.069 -10000 0 -0.12 32 32
RAS family/GDP -0.005 0.011 -10000 0 -10000 0 0
MAP3K14 0.002 0.13 -10000 0 -0.28 39 39
PDPK1 -0.022 0.19 -10000 0 -0.43 42 42
TCR/CD3/MHC I/CD8/Fyn -0.11 0.38 -10000 0 -0.9 43 43
Calcium signaling in the CD4+ TCR pathway

Figure S34.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S34.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.012 0.087 -9999 0 -0.38 13 13
NFATC2 -0.058 0.14 -9999 0 -0.37 46 46
NFATC3 0.007 0.028 -9999 0 -10000 0 0
CD40LG -0.25 0.33 -9999 0 -0.71 69 69
PTGS2 -0.28 0.35 -9999 0 -0.7 89 89
JUNB 0.009 0.061 -9999 0 -0.57 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.005 0.011 -9999 0 -10000 0 0
CaM/Ca2+ -0.005 0.011 -9999 0 -10000 0 0
CALM1 0.011 0.008 -9999 0 -10000 0 0
JUN -0.004 0.095 -9999 0 -0.58 7 7
mol:Ca2+ -0.008 0.011 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.003 0.004 -9999 0 -10000 0 0
FOSL1 -0.026 0.15 -9999 0 -0.57 19 19
CREM 0.015 0 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.13 0.17 -9999 0 -0.47 38 38
FOS -0.16 0.27 -9999 0 -0.58 80 80
IFNG -0.26 0.32 -9999 0 -0.7 68 68
AP-1/NFAT1-c-4 -0.28 0.37 -9999 0 -0.72 81 81
FASLG -0.24 0.32 -9999 0 -0.71 62 62
NFAT1-c-4/ICER1 -0.074 0.15 -9999 0 -0.39 37 37
IL2RA -0.24 0.33 -9999 0 -0.75 59 59
FKBP12/FK506 0.011 0 -9999 0 -10000 0 0
CSF2 -0.26 0.32 -9999 0 -0.68 73 73
JunB/Fra1/NFAT1-c-4 -0.1 0.17 -9999 0 -0.43 38 38
IL4 -0.23 0.3 -9999 0 -0.69 52 52
IL2 -0.008 0.019 -9999 0 -10000 0 0
IL3 -0.023 0.023 -9999 0 -10000 0 0
FKBP1A 0.015 0 -9999 0 -10000 0 0
BATF3 0.007 0.068 -9999 0 -0.55 4 4
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.015 0.002 -9999 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

Figure S35.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S35.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.02 0.029 -9999 0 -10000 0 0
VDR 0.011 0.047 -9999 0 -0.52 2 2
FAM120B 0.015 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.021 0.13 -9999 0 -0.4 5 5
RXRs/LXRs/DNA/Oxysterols -0.002 0.12 -9999 0 -0.38 5 5
MED1 0.015 0 -9999 0 -10000 0 0
mol:9cRA 0.006 0.007 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.006 0.1 -9999 0 -0.5 4 4
RXRs/NUR77 -0.23 0.22 -9999 0 -0.37 181 181
RXRs/PPAR -0.06 0.15 -9999 0 -0.25 96 96
NCOR2 0.015 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 0.008 0.034 -9999 0 -0.38 2 2
RARs/VDR/DNA/Vit D3 0.009 0.088 -9999 0 -0.28 22 22
RARA 0.015 0 -9999 0 -10000 0 0
NCOA1 0.015 0 -9999 0 -10000 0 0
VDR/VDR/DNA 0.011 0.047 -9999 0 -0.52 2 2
RARs/RARs/DNA/9cRA 0.005 0.085 -9999 0 -0.29 21 21
RARG 0.015 0 -9999 0 -10000 0 0
RPS6KB1 0.03 0.044 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT 0.006 0.1 -9999 0 -0.5 4 4
THRA 0.015 0 -9999 0 -10000 0 0
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA 0.008 0.034 -9999 0 -0.38 2 2
RXRs/PPAR/9cRA/PGJ2/DNA -0.055 0.16 -9999 0 -0.3 78 78
NR1H4 -0.13 0.24 -9999 0 -0.55 65 65
RXRs/LXRs/DNA -0.025 0.15 -9999 0 -0.38 5 5
NR1H2 0.022 0.005 -9999 0 -10000 0 0
NR1H3 0.022 0.005 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.05 0.15 -9999 0 -0.28 79 79
NR4A1 -0.3 0.29 -9999 0 -0.57 147 147
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.092 0.16 -9999 0 -0.27 110 110
RXRG -0.16 0.26 -9999 0 -0.56 78 78
RXR alpha/CCPG 0.025 0.027 -9999 0 -0.4 1 1
RXRA 0.019 0.036 -9999 0 -0.56 1 1
RXRB 0.021 0.005 -9999 0 -10000 0 0
THRB -0.015 0.13 -9999 0 -0.57 14 14
PPARG -0.034 0.16 -9999 0 -0.56 23 23
PPARD 0.015 0 -9999 0 -10000 0 0
TNF 0.002 0.12 -9999 0 -0.46 5 5
mol:Oxysterols 0.006 0.006 -9999 0 -10000 0 0
cholesterol transport -0.001 0.12 -9999 0 -0.38 5 5
PPARA 0.011 0.05 -9999 0 -0.57 2 2
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB -0.031 0.16 -9999 0 -0.57 21 21
RXRs/NUR77/BCL2 -0.21 0.2 -9999 0 -0.33 183 183
SREBF1 0.008 0.11 -9999 0 -0.46 1 1
RXRs/RXRs/DNA/9cRA -0.055 0.16 -9999 0 -0.3 78 78
ABCA1 0.009 0.11 -9999 0 -0.46 1 1
RARs/THRs 0.004 0.12 -9999 0 -0.57 4 4
RXRs/FXR -0.13 0.21 -9999 0 -0.36 112 112
BCL2 -0.011 0.12 -9999 0 -0.57 12 12
Neurotrophic factor-mediated Trk receptor signaling

Figure S36.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S36.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.011 0.043 -10000 0 -0.48 2 2
RAS family/GTP/Tiam1 -0.086 0.11 -10000 0 -0.27 33 33
NT3 (dimer)/TRKC -0.26 0.27 -10000 0 -0.48 151 151
NT3 (dimer)/TRKB -0.27 0.3 -10000 0 -0.49 152 152
SHC/Grb2/SOS1/GAB1/PI3K 0.042 0.009 -10000 0 -10000 0 0
RAPGEF1 0.015 0 -10000 0 -10000 0 0
BDNF -0.094 0.23 -10000 0 -0.57 50 50
PIK3CA 0.015 0 -10000 0 -10000 0 0
DYNLT1 0.015 0 -10000 0 -10000 0 0
NTRK1 0.006 0.061 -10000 0 -0.48 4 4
NTRK2 -0.22 0.28 -10000 0 -0.56 111 111
NTRK3 -0.27 0.29 -10000 0 -0.57 132 132
NT-4/5 (dimer)/TRKB -0.23 0.27 -10000 0 -0.45 145 145
neuron apoptosis 0.19 0.25 0.52 80 -10000 0 80
SHC 2-3/Grb2 -0.21 0.28 -10000 0 -0.58 80 80
SHC1 0.013 0.03 -10000 0 -0.48 1 1
SHC2 -0.21 0.28 -10000 0 -0.63 66 66
SHC3 -0.22 0.26 -10000 0 -0.59 76 76
STAT3 (dimer) 0.013 0.056 -10000 0 -0.34 4 4
NT3 (dimer)/TRKA -0.13 0.22 -10000 0 -0.39 103 103
RIN/GDP -0.067 0.1 -10000 0 -0.24 24 24
GIPC1 0.015 0 -10000 0 -10000 0 0
KRAS 0.013 0.03 -10000 0 -0.48 1 1
DNAJA3 -0.1 0.16 -10000 0 -0.36 61 61
RIN/GTP 0 0.021 -10000 0 -0.35 1 1
CCND1 0.011 0.12 -10000 0 -0.5 12 12
MAGED1 0.015 0 -10000 0 -10000 0 0
PTPN11 0.015 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.033 0.16 -10000 0 -0.56 22 22
SHC/GRB2/SOS1 0.03 0.019 -10000 0 -0.27 1 1
GRB2 0.015 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.052 0.16 -10000 0 -0.36 56 56
TRKA/NEDD4-2 0.016 0.044 -10000 0 -0.34 4 4
ELMO1 0.011 0.05 -10000 0 -0.57 2 2
RhoG/GTP/ELMO1/DOCK1 0.017 0.047 -10000 0 -0.51 2 2
NGF -0.062 0.2 -10000 0 -0.57 35 35
HRAS 0.015 0 -10000 0 -10000 0 0
DOCK1 0.013 0.036 -10000 0 -0.57 1 1
GAB2 0.015 0 -10000 0 -10000 0 0
RIT2 -0.001 0.03 -10000 0 -0.48 1 1
RIT1 0.015 0 -10000 0 -10000 0 0
FRS2 0.006 0.068 -10000 0 -0.48 5 5
DNM1 0.004 0.079 -10000 0 -0.57 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.015 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.1 0.16 -10000 0 -0.36 63 63
mol:GDP -0.099 0.15 -10000 0 -0.34 34 34
NGF (dimer) -0.061 0.2 -10000 0 -0.56 35 35
RhoG/GDP 0.008 0.037 -10000 0 -0.42 2 2
RIT1/GDP -0.061 0.1 -10000 0 -0.24 24 24
TIAM1 0.013 0.036 -10000 0 -0.57 1 1
PIK3R1 0.015 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.18 0.24 -10000 0 -0.4 132 132
KIDINS220/CRKL/C3G 0.02 0.031 -10000 0 -0.34 2 2
SHC/RasGAP 0.021 0.022 -10000 0 -0.34 1 1
FRS2 family/SHP2 0.025 0.041 -10000 0 -0.27 5 5
SHC/GRB2/SOS1/GAB1 0.038 0.017 -10000 0 -10000 0 0
RIT1/GTP 0.011 0 -10000 0 -10000 0 0
NT3 (dimer) -0.096 0.23 -10000 0 -0.56 51 51
RAP1/GDP -0.069 0.069 -10000 0 -0.21 13 13
KIDINS220/CRKL 0.011 0.043 -10000 0 -0.48 2 2
BDNF (dimer) -0.094 0.23 -10000 0 -0.56 50 50
ubiquitin-dependent protein catabolic process -0.023 0.13 -10000 0 -0.33 39 39
Schwann cell development -0.054 0.037 -10000 0 -10000 0 0
EHD4 0.015 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.034 0.038 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.043 0.019 -10000 0 -10000 0 0
RAP1B 0.015 0 -10000 0 -10000 0 0
RAP1A 0.015 0 -10000 0 -10000 0 0
CDC42/GTP -0.33 0.28 -10000 0 -0.62 114 114
ABL1 0.015 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.022 0 -10000 0 -10000 0 0
Rap1/GTP -0.065 0.073 -10000 0 -10000 0 0
STAT3 0.013 0.056 -10000 0 -0.34 4 4
axon guidance -0.31 0.26 -10000 0 -0.58 114 114
MAPK3 -0.038 0.15 -10000 0 -0.32 56 56
MAPK1 -0.038 0.15 -10000 0 -0.33 48 48
CDC42/GDP -0.061 0.1 -10000 0 -0.24 24 24
NTF3 -0.096 0.23 -10000 0 -0.56 51 51
NTF4 -0.033 0.16 -10000 0 -0.57 22 22
NGF (dimer)/TRKA/FAIM -0.023 0.13 -10000 0 -0.33 39 39
PI3K 0.022 0 -10000 0 -10000 0 0
FRS3 0.015 0 -10000 0 -10000 0 0
FAIM 0.015 0 -10000 0 -10000 0 0
GAB1 0.015 0 -10000 0 -10000 0 0
RASGRF1 -0.14 0.17 -10000 0 -0.37 65 65
SOS1 0.015 0 -10000 0 -10000 0 0
MCF2L -0.23 0.25 -10000 0 -0.43 152 152
RGS19 0.015 0 -10000 0 -10000 0 0
CDC42 0.015 0 -10000 0 -10000 0 0
RAS family/GTP 0.008 0.071 -10000 0 -10000 0 0
Rac1/GDP -0.061 0.1 -10000 0 -0.24 24 24
NGF (dimer)/TRKA/GRIT -0.033 0.13 -10000 0 -0.34 39 39
neuron projection morphogenesis -0.074 0.18 -10000 0 -0.52 16 16
NGF (dimer)/TRKA/NEDD4-2 -0.023 0.13 -10000 0 -0.33 39 39
MAP2K1 0.043 0.016 -10000 0 -10000 0 0
NGFR -0.12 0.25 -10000 0 -0.56 65 65
NGF (dimer)/TRKA/GIPC/GAIP -0.002 0.11 -10000 0 -0.26 37 37
RAS family/GTP/PI3K 0.035 0.009 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0.04 0.035 -10000 0 -10000 0 0
NRAS 0.015 0 -10000 0 -10000 0 0
GRB2/SOS1 0.022 0 -10000 0 -10000 0 0
PRKCI 0.015 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.015 0 -10000 0 -10000 0 0
PRKCZ 0.013 0.036 -10000 0 -0.57 1 1
MAPKKK cascade -0.13 0.24 -10000 0 -0.72 35 35
RASA1 0.015 0 -10000 0 -10000 0 0
TRKA/c-Abl 0.016 0.044 -10000 0 -0.34 4 4
SQSTM1 0.015 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.16 0.22 -10000 0 -0.37 127 127
NGF (dimer)/TRKA/p62/Atypical PKCs -0.003 0.12 -10000 0 -0.28 35 35
MATK -0.032 0.16 -10000 0 -0.55 22 22
NEDD4L 0.015 0 -10000 0 -10000 0 0
RAS family/GDP -0.065 0.065 -10000 0 -0.22 5 5
NGF (dimer)/TRKA -0.11 0.17 -10000 0 -0.35 84 84
Rac1/GTP -0.12 0.11 -10000 0 -0.29 56 56
FRS2 family/SHP2/CRK family 0.038 0.042 -10000 0 -10000 0 0
S1P1 pathway

Figure S37.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S37.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.018 0.01 -9999 0 -10000 0 0
PDGFRB 0.001 0.08 -9999 0 -0.57 5 5
SPHK1 -0.033 0.071 -9999 0 -1.1 1 1
mol:S1P -0.039 0.072 -9999 0 -0.66 2 2
S1P1/S1P/Gi -0.18 0.26 -9999 0 -0.47 97 97
GNAO1 -0.16 0.27 -9999 0 -0.57 80 80
PDGFB-D/PDGFRB/PLCgamma1 -0.15 0.24 -9999 0 -0.49 64 64
PLCG1 -0.16 0.24 -9999 0 -0.44 97 97
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.001 0.08 -9999 0 -0.57 5 5
GNAI2 0.012 0.007 -9999 0 -10000 0 0
GNAI3 0.012 0.007 -9999 0 -10000 0 0
GNAI1 0.01 0.036 -9999 0 -0.57 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.016 0.013 -9999 0 -10000 0 0
S1P1/S1P -0.039 0.071 -9999 0 -0.53 2 2
negative regulation of cAMP metabolic process -0.17 0.25 -9999 0 -0.46 97 97
MAPK3 -0.2 0.31 -9999 0 -0.57 96 96
calcium-dependent phospholipase C activity -0.003 0.004 -9999 0 -10000 0 0
Rac1/GDP 0.011 0 -9999 0 -10000 0 0
RhoA/GDP 0.011 0 -9999 0 -10000 0 0
KDR 0.014 0.004 -9999 0 -10000 0 0
PLCB2 -0.011 0.08 -9999 0 -0.4 3 3
RAC1 0.015 0 -9999 0 -10000 0 0
RhoA/GTP -0.031 0.059 -9999 0 -0.43 2 2
receptor internalization -0.037 0.067 -9999 0 -0.49 2 2
PTGS2 -0.29 0.46 -9999 0 -0.84 96 96
Rac1/GTP -0.031 0.059 -9999 0 -0.43 2 2
RHOA 0.015 0 -9999 0 -10000 0 0
VEGFA 0.014 0.004 -9999 0 -10000 0 0
negative regulation of T cell proliferation -0.17 0.25 -9999 0 -0.46 97 97
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ -0.12 0.24 -9999 0 -0.57 60 60
MAPK1 -0.2 0.31 -9999 0 -0.57 96 96
S1P1/S1P/PDGFB-D/PDGFRB -0.027 0.11 -9999 0 -0.49 5 5
ABCC1 0.009 0.043 -9999 0 -0.49 2 2
LPA receptor mediated events

Figure S38.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S38.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.009 0.13 -9999 0 -0.41 16 16
NF kappa B1 p50/RelA/I kappa B alpha 0.007 0.11 -9999 0 -0.34 6 6
AP1 -0.14 0.2 -9999 0 -0.5 42 42
mol:PIP3 -0.06 0.12 -9999 0 -0.43 17 17
AKT1 0.033 0.095 -9999 0 -0.4 6 6
PTK2B -0.006 0.1 -9999 0 -0.27 22 22
RHOA 0.017 0.05 -9999 0 -0.26 1 1
PIK3CB 0.015 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.005 0.1 -9999 0 -0.34 6 6
MAGI3 0.015 0 -9999 0 -10000 0 0
RELA 0.015 0 -9999 0 -10000 0 0
apoptosis -0.036 0.15 -9999 0 -0.35 35 35
HRAS/GDP 0.011 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization -0.013 0.12 -9999 0 -0.32 20 20
NF kappa B1 p50/RelA -0.052 0.12 -9999 0 -0.43 13 13
endothelial cell migration -0.049 0.22 -9999 0 -0.61 34 34
ADCY4 -0.1 0.21 -9999 0 -0.43 59 59
ADCY5 -0.23 0.3 -9999 0 -0.55 103 103
ADCY6 -0.1 0.21 -9999 0 -0.43 59 59
ADCY7 -0.1 0.21 -9999 0 -0.43 59 59
ADCY1 -0.1 0.21 -9999 0 -0.42 63 63
ADCY2 -0.19 0.28 -9999 0 -0.52 94 94
ADCY3 -0.1 0.21 -9999 0 -0.43 59 59
ADCY8 -0.1 0.21 -9999 0 -0.43 59 59
ADCY9 -0.11 0.22 -9999 0 -0.44 60 60
GSK3B 0.003 0.095 -9999 0 -0.32 10 10
arachidonic acid secretion -0.1 0.21 -9999 0 -0.43 60 60
GNG2 0.008 0.061 -9999 0 -0.56 3 3
TRIP6 0.022 0.024 -9999 0 -10000 0 0
GNAO1 -0.12 0.22 -9999 0 -0.38 100 100
HRAS 0.015 0 -9999 0 -10000 0 0
NFKBIA -0.003 0.12 -9999 0 -0.39 7 7
GAB1 0.015 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly 0 0.057 -9999 0 -0.92 1 1
JUN 0 0.093 -9999 0 -0.57 7 7
LPA/LPA2/NHERF2 -0.01 0.039 -9999 0 -0.31 3 3
TIAM1 -0.001 0.067 -9999 0 -1.1 1 1
PIK3R1 0.015 0.001 -9999 0 -10000 0 0
mol:IP3 -0.006 0.1 -9999 0 -0.35 6 6
PLCB3 0.021 0.04 -9999 0 -0.27 3 3
FOS -0.16 0.27 -9999 0 -0.57 80 80
positive regulation of mitosis -0.1 0.21 -9999 0 -0.43 60 60
LPA/LPA1-2-3 -0.042 0.16 -9999 0 -0.36 41 41
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0.001 -9999 0 -10000 0 0
BCAR1 0.015 0 -9999 0 -10000 0 0
stress fiber formation -0.007 0.12 -9999 0 -0.37 13 13
GNAZ -0.095 0.2 -9999 0 -0.37 84 84
EGFR/PI3K-beta/Gab1 -0.062 0.13 -9999 0 -0.45 17 17
positive regulation of dendritic cell cytokine production -0.069 0.14 -9999 0 -0.37 37 37
LPA/LPA2/MAGI-3 -0.008 0.039 -9999 0 -0.31 3 3
ARHGEF1 0.005 0.11 -9999 0 -0.36 14 14
GNAI2 -0.014 0.13 -9999 0 -0.33 34 34
GNAI3 -0.014 0.13 -9999 0 -0.33 34 34
GNAI1 -0.015 0.13 -9999 0 -0.33 35 35
LPA/LPA3 -0.049 0.12 -9999 0 -0.41 27 27
LPA/LPA2 -0.012 0.049 -9999 0 -0.38 3 3
LPA/LPA1 -0.05 0.14 -9999 0 -0.39 34 34
HB-EGF/EGFR -0.085 0.17 -9999 0 -0.31 87 87
HBEGF -0.092 0.18 -9999 0 -0.36 82 82
mol:DAG -0.006 0.1 -9999 0 -0.35 6 6
cAMP biosynthetic process -0.15 0.25 -9999 0 -0.44 93 93
NFKB1 0.015 0 -9999 0 -10000 0 0
SRC 0.015 0 -9999 0 -10000 0 0
GNB1 0.015 0.001 -9999 0 -10000 0 0
LYN -0.003 0.12 -9999 0 -0.39 7 7
GNAQ -0.013 0.097 -9999 0 -0.29 25 25
LPAR2 0.009 0.053 -9999 0 -0.48 3 3
LPAR3 -0.043 0.17 -9999 0 -0.55 27 27
LPAR1 -0.027 0.15 -9999 0 -0.62 14 14
IL8 -0.12 0.23 -9999 0 -0.5 56 56
PTK2 -0.029 0.15 -9999 0 -0.35 36 36
Rac1/GDP 0.011 0 -9999 0 -10000 0 0
CASP3 -0.037 0.15 -9999 0 -0.36 35 35
EGFR -0.007 0.11 -9999 0 -0.52 11 11
PLCG1 -0.026 0.12 -9999 0 -0.29 35 35
PLD2 -0.029 0.15 -9999 0 -0.35 36 36
G12/G13 -0.004 0.12 -9999 0 -0.39 14 14
PI3K-beta -0.029 0.086 -9999 0 -0.47 6 6
cell migration -0.017 0.051 -9999 0 -0.21 4 4
SLC9A3R2 0.015 0 -9999 0 -10000 0 0
PXN -0.008 0.12 -9999 0 -0.38 13 13
HRAS/GTP -0.11 0.22 -9999 0 -0.44 60 60
RAC1 0.015 0 -9999 0 -10000 0 0
MMP9 -0.13 0.23 -9999 0 -0.49 77 77
PRKCE 0.015 0 -9999 0 -10000 0 0
PRKCD 0.003 0.097 -9999 0 -0.34 5 5
Gi(beta/gamma) -0.099 0.21 -9999 0 -0.42 60 60
mol:LPA -0.011 0.052 -9999 0 -0.19 20 20
TRIP6/p130 Cas/FAK1/Paxillin -0.047 0.12 -9999 0 -0.47 11 11
MAPKKK cascade -0.1 0.21 -9999 0 -0.43 60 60
contractile ring contraction involved in cytokinesis 0.017 0.05 -9999 0 -0.25 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.064 0.16 -9999 0 -0.32 65 65
GNA15 -0.015 0.1 -9999 0 -0.29 27 27
GNA12 0.015 0 -9999 0 -10000 0 0
GNA13 0.015 0 -9999 0 -10000 0 0
MAPT -0.014 0.12 -9999 0 -0.32 20 20
GNA11 -0.014 0.1 -9999 0 -0.31 25 25
Rac1/GTP 0.026 0.062 -9999 0 -0.98 1 1
MMP2 -0.05 0.22 -9999 0 -0.61 34 34
IL6-mediated signaling events

Figure S39.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S39.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.053 0.24 -10000 0 -0.71 12 12
CRP -0.06 0.24 -10000 0 -0.75 12 12
cell cycle arrest -0.062 0.27 -10000 0 -0.67 31 31
TIMP1 -0.044 0.21 -10000 0 -0.61 10 10
IL6ST -0.07 0.21 -10000 0 -0.57 41 41
Rac1/GDP -0.13 0.27 -10000 0 -0.56 58 58
AP1 -0.05 0.16 -10000 0 -0.45 12 12
GAB2 0.018 0.007 -10000 0 -10000 0 0
TNFSF11 -0.06 0.25 -10000 0 -0.79 11 11
HSP90B1 0.023 0.059 -10000 0 -0.56 1 1
GAB1 0.017 0.004 -10000 0 -10000 0 0
MAPK14 -0.17 0.32 -10000 0 -0.73 52 52
AKT1 0.063 0.015 -10000 0 -10000 0 0
FOXO1 0.068 0.013 -10000 0 -10000 0 0
MAP2K6 -0.16 0.3 -10000 0 -0.67 51 51
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
MAP2K4 -0.096 0.27 -10000 0 -0.61 41 41
MITF -0.16 0.3 -10000 0 -0.61 62 62
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.015 0 -10000 0 -10000 0 0
A2M -0.088 0.39 -10000 0 -1.4 21 21
CEBPB 0.021 0.036 -10000 0 -0.56 1 1
GRB2/SOS1/GAB family/SHP2 -0.015 0.099 0.25 3 -0.27 1 4
STAT3 -0.074 0.29 -10000 0 -0.72 31 31
STAT1 -0.006 0.019 -10000 0 -10000 0 0
CEBPD -0.055 0.25 -10000 0 -0.77 12 12
PIK3CA 0.017 0 -10000 0 -10000 0 0
PI3K 0.026 0.001 -10000 0 -10000 0 0
JUN 0 0.093 -10000 0 -0.57 7 7
PIAS3/MITF -0.15 0.28 -10000 0 -0.6 56 56
MAPK11 -0.17 0.32 -10000 0 -0.73 52 52
STAT3 (dimer)/FOXO1 -0.023 0.24 -10000 0 -0.6 18 18
GRB2/SOS1/GAB family -0.14 0.22 0.21 3 -0.58 41 44
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.16 0.28 -10000 0 -0.54 68 68
GRB2 0.017 0.004 -10000 0 -10000 0 0
JAK2 0.013 0.036 -10000 0 -0.57 1 1
LBP -0.061 0.21 -10000 0 -0.61 8 8
PIK3R1 0.016 0 -10000 0 -10000 0 0
JAK1 0.017 0.006 -10000 0 -10000 0 0
MYC -0.079 0.31 -10000 0 -0.96 20 20
FGG -0.073 0.25 -10000 0 -0.8 11 11
macrophage differentiation -0.062 0.27 -10000 0 -0.67 31 31
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.19 0.24 -10000 0 -0.55 55 55
JUNB -0.056 0.24 -10000 0 -0.69 17 17
FOS -0.16 0.27 -10000 0 -0.57 80 80
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.16 0.29 -10000 0 -0.59 58 58
STAT1/PIAS1 -0.12 0.25 -10000 0 -0.57 42 42
GRB2/SOS1/GAB family/SHP2/PI3K 0.05 0.017 -10000 0 -10000 0 0
STAT3 (dimer) -0.07 0.28 -10000 0 -0.7 31 31
PRKCD -0.067 0.26 -10000 0 -0.6 36 36
IL6R -0.031 0.16 -10000 0 -0.56 22 22
SOCS3 -0.21 0.42 -10000 0 -1.1 43 43
gp130 (dimer)/JAK1/JAK1/LMO4 -0.015 0.14 -10000 0 -0.34 42 42
Rac1/GTP -0.12 0.28 -10000 0 -0.57 56 56
HCK -0.01 0.12 -10000 0 -0.55 12 12
MAPKKK cascade 0.022 0.076 -10000 0 -10000 0 0
bone resorption -0.055 0.24 -10000 0 -0.72 12 12
IRF1 -0.052 0.24 -10000 0 -0.7 13 13
mol:GDP -0.15 0.28 -10000 0 -0.6 58 58
SOS1 0.017 0.006 -10000 0 -10000 0 0
VAV1 -0.15 0.29 -10000 0 -0.61 58 58
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.2 0.36 -10000 0 -0.81 52 52
PTPN11 -0.005 0.018 -10000 0 -10000 0 0
IL6/IL6RA -0.2 0.26 -10000 0 -0.45 125 125
gp130 (dimer)/TYK2/TYK2/LMO4 -0.021 0.14 -10000 0 -0.34 42 42
gp130 (dimer)/JAK2/JAK2/LMO4 -0.022 0.14 -10000 0 -0.35 42 42
IL6 -0.24 0.29 -10000 0 -0.56 121 121
PIAS3 0.015 0 -10000 0 -10000 0 0
PTPRE 0.004 0.046 -10000 0 -0.51 2 2
PIAS1 0.015 0 -10000 0 -10000 0 0
RAC1 0.016 0.001 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.17 0.26 -10000 0 -0.48 77 77
LMO4 0.017 0.037 -10000 0 -0.57 1 1
STAT3 (dimer)/PIAS3 -0.14 0.23 -10000 0 -0.68 35 35
MCL1 0.068 0.014 -10000 0 -10000 0 0
S1P5 pathway

Figure S40.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S40.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.11 0.16 0.42 42 -10000 0 42
GNAI2 0.015 0 -10000 0 -10000 0 0
S1P/S1P5/G12 0.006 0.065 -10000 0 -0.29 12 12
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.16 0.27 -10000 0 -0.57 80 80
RhoA/GTP -0.089 0.18 -10000 0 -0.43 42 42
negative regulation of cAMP metabolic process -0.1 0.19 -10000 0 -0.36 82 82
GNAZ -0.12 0.24 -10000 0 -0.57 60 60
GNAI3 0.015 0 -10000 0 -10000 0 0
GNA12 0.015 0 -10000 0 -10000 0 0
S1PR5 -0.008 0.11 -10000 0 -0.5 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.1 0.2 -10000 0 -0.36 82 82
RhoA/GDP 0.011 0 -10000 0 -10000 0 0
RHOA 0.015 0 -10000 0 -10000 0 0
GNAI1 0.013 0.036 -10000 0 -0.57 1 1
Visual signal transduction: Cones

Figure S41.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S41.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Cone Metarhodopsin II/Cone Transducin 0.016 0.052 -9999 0 -0.28 8 8
RGS9BP -0.013 0.12 -9999 0 -0.55 13 13
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0.001 0.004 -9999 0 -10000 0 0
mol:Na + -0.096 0.17 -9999 0 -0.32 88 88
mol:ADP 0.01 0.023 -9999 0 -0.35 1 1
GNAT2 0.009 0.043 -9999 0 -0.48 2 2
RGS9-1/Gbeta5/R9AP -0.065 0.17 -9999 0 -0.35 67 67
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0.007 0.032 -9999 0 -0.29 3 3
GRK7 0.01 0.031 -9999 0 -0.48 1 1
CNGB3 -0.12 0.22 -9999 0 -0.48 71 71
Cone Metarhodopsin II/X-Arrestin 0.002 0.004 -9999 0 -10000 0 0
mol:Ca2+ -0.095 0.16 -9999 0 -0.3 97 97
Cone PDE6 -0.053 0.14 -9999 0 -0.31 44 44
Cone Metarhodopsin II 0.008 0.017 -9999 0 -0.26 1 1
Na + (4 Units) -0.095 0.16 -9999 0 -0.3 97 97
GNAT2/GDP -0.05 0.14 -9999 0 -0.29 65 65
GNB5 0.015 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.008 0.029 -9999 0 -0.26 3 3
Cone Transducin 0.018 0.055 -9999 0 -0.29 8 8
SLC24A2 -0.017 0.11 -9999 0 -0.48 15 15
GNB3/GNGT2 0.013 0.063 -9999 0 -0.41 6 6
GNB3 0.009 0.061 -9999 0 -0.57 3 3
GNAT2/GTP 0.007 0.031 -9999 0 -0.35 2 2
CNGA3 -0.042 0.16 -9999 0 -0.57 24 24
ARR3 0.003 0.006 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.096 0.17 -9999 0 -0.32 88 88
mol:Pi -0.065 0.17 -9999 0 -0.35 67 67
Cone CNG Channel -0.087 0.13 -9999 0 -0.48 8 8
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.017 0.11 -9999 0 -0.48 15 15
RGS9 -0.11 0.24 -9999 0 -0.57 57 57
PDE6C 0.003 0.006 -9999 0 -10000 0 0
GNGT2 0.008 0.061 -9999 0 -0.57 3 3
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.001 0.03 -9999 0 -0.48 1 1
Lissencephaly gene (LIS1) in neuronal migration and development

Figure S42.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S42.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
DYNC1H1 0.015 0 -9999 0 -10000 0 0
VLDLR -0.002 0.099 -9999 0 -0.57 8 8
LRPAP1 0.013 0.03 -9999 0 -0.48 1 1
NUDC 0.015 0 -9999 0 -10000 0 0
RELN/LRP8 -0.15 0.21 -9999 0 -0.37 120 120
CaM/Ca2+ 0.011 0 -9999 0 -10000 0 0
KATNA1 0.015 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.13 0.19 -9999 0 -0.35 92 92
IQGAP1/CaM 0.022 0 -9999 0 -10000 0 0
DAB1 -0.07 0.19 -9999 0 -0.53 39 39
IQGAP1 0.015 0 -9999 0 -10000 0 0
PLA2G7 -0.06 0.18 -9999 0 -0.48 40 40
CALM1 0.015 0 -9999 0 -10000 0 0
DYNLT1 0.015 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.042 0.14 -9999 0 -0.34 48 48
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.015 0 -9999 0 -10000 0 0
CDK5R1 -0.015 0.12 -9999 0 -0.48 16 16
LIS1/Poliovirus Protein 3A 0.019 0 -9999 0 -10000 0 0
CDK5R2 -0.017 0.11 -9999 0 -0.48 15 15
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.16 0.22 -9999 0 -0.38 122 122
YWHAE 0.013 0.036 -9999 0 -0.57 1 1
NDEL1/14-3-3 E -0.086 0.17 -9999 0 -0.43 26 26
MAP1B -0.03 0.091 -9999 0 -0.31 26 26
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.11 0.19 -9999 0 -0.51 27 27
RELN -0.19 0.27 -9999 0 -0.56 93 93
PAFAH/LIS1 -0.015 0.11 -9999 0 -0.27 40 40
LIS1/CLIP170 0.03 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.086 0.11 -9999 0 -0.35 21 21
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.1 0.17 -9999 0 -0.34 58 58
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.098 0.18 -9999 0 -0.46 27 27
LIS1/IQGAP1 0.03 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.026 0 -9999 0 -10000 0 0
PAFAH1B3 -0.02 0.13 -9999 0 -0.48 19 19
PAFAH1B2 0.015 0 -9999 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.008 0.063 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.075 0.16 -9999 0 -0.42 22 22
LRP8 -0.073 0.19 -9999 0 -0.48 47 47
NDEL1/Katanin 60 -0.084 0.17 -9999 0 -0.43 26 26
P39/CDK5 -0.11 0.18 -9999 0 -0.49 27 27
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.03 0 -9999 0 -10000 0 0
CDK5 -0.11 0.18 -9999 0 -0.5 21 21
PPP2R5D 0.015 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.026 0 -9999 0 -10000 0 0
CSNK2A1 0.015 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.12 0.19 -9999 0 -0.32 110 110
RELN/VLDLR -0.14 0.2 -9999 0 -0.37 97 97
CDC42 0 0 -9999 0 -10000 0 0
LPA4-mediated signaling events

Figure S43.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S43.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 0.02 0.022 -9999 0 -0.35 1 1
ADCY5 -0.17 0.18 -9999 0 -0.35 136 136
ADCY6 0.022 0 -9999 0 -10000 0 0
ADCY7 0.022 0 -9999 0 -10000 0 0
ADCY1 0.014 0.05 -9999 0 -0.29 7 7
ADCY2 -0.11 0.18 -9999 0 -0.35 98 98
ADCY3 0.022 0 -9999 0 -10000 0 0
ADCY8 0.013 0.019 -9999 0 -0.28 1 1
PRKCE 0.013 0 -9999 0 -10000 0 0
ADCY9 0.016 0.045 -9999 0 -0.35 4 4
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.059 0.093 -9999 0 -0.27 5 5
IL12-mediated signaling events

Figure S44.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S44.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.011 0.12 -10000 0 -0.34 15 15
TBX21 -0.13 0.46 -10000 0 -1.1 38 38
B2M 0.015 0.008 -10000 0 -10000 0 0
TYK2 0.016 0.022 -10000 0 -10000 0 0
IL12RB1 -0.019 0.14 -10000 0 -0.52 18 18
GADD45B -0.076 0.38 -10000 0 -0.98 27 27
IL12RB2 -0.079 0.2 -10000 0 -0.5 50 50
GADD45G -0.079 0.37 -10000 0 -0.96 28 28
natural killer cell activation 0.001 0.025 -10000 0 -10000 0 0
RELB 0.015 0 -10000 0 -10000 0 0
RELA 0.015 0 -10000 0 -10000 0 0
IL18 0.007 0.081 -10000 0 -0.58 5 5
IL2RA -0.044 0.17 -10000 0 -0.53 29 29
IFNG -0.078 0.19 -10000 0 -0.48 48 48
STAT3 (dimer) -0.073 0.34 -10000 0 -0.72 44 44
HLA-DRB5 -0.028 0.14 -10000 0 -0.54 19 19
FASLG -0.15 0.49 -10000 0 -1.1 44 44
NF kappa B2 p52/RelB -0.19 0.37 -10000 0 -0.88 47 47
CD4 0.007 0.05 -10000 0 -0.57 2 2
SOCS1 0.013 0.03 -10000 0 -0.48 1 1
EntrezGene:6955 -0.006 0.015 -10000 0 -10000 0 0
CD3D -0.047 0.17 -10000 0 -0.56 27 27
CD3E -0.049 0.18 -10000 0 -0.57 28 28
CD3G -0.052 0.18 -10000 0 -0.57 29 29
IL12Rbeta2/JAK2 -0.046 0.15 -10000 0 -0.35 51 51
CCL3 -0.14 0.48 -10000 0 -1.1 41 41
CCL4 -0.16 0.52 -10000 0 -1.2 42 42
HLA-A 0.013 0.036 -10000 0 -0.57 1 1
IL18/IL18R 0.029 0.13 -10000 0 -0.4 19 19
NOS2 -0.11 0.41 -10000 0 -1.1 30 30
IL12/IL12R/TYK2/JAK2/SPHK2 -0.012 0.12 -10000 0 -0.33 15 15
IL1R1 -0.11 0.42 -10000 0 -1 34 34
IL4 0.001 0.025 -10000 0 -10000 0 0
JAK2 0.014 0.042 -10000 0 -0.57 1 1
EntrezGene:6957 -0.005 0.014 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.12 0.37 -10000 0 -0.8 47 47
RAB7A -0.032 0.3 -10000 0 -0.71 29 29
lysosomal transport -0.026 0.29 -10000 0 -0.67 29 29
FOS -0.4 0.65 -10000 0 -1.2 98 98
STAT4 (dimer) -0.071 0.38 -10000 0 -0.78 46 46
STAT5A (dimer) -0.21 0.38 -10000 0 -0.89 50 50
GZMA -0.16 0.52 -10000 0 -1.2 40 40
GZMB -0.14 0.47 -10000 0 -1.2 31 31
HLX 0.015 0 -10000 0 -10000 0 0
LCK -0.13 0.47 -10000 0 -1 45 45
TCR/CD3/MHC II/CD4 -0.12 0.29 -10000 0 -0.64 45 45
IL2/IL2R -0.022 0.15 -10000 0 -0.41 23 23
MAPK14 -0.062 0.37 -10000 0 -0.86 33 33
CCR5 -0.098 0.42 -10000 0 -0.99 35 35
IL1B -0.036 0.16 -10000 0 -0.53 26 26
STAT6 -0.012 0.14 -10000 0 -0.35 15 15
STAT4 -0.013 0.12 -10000 0 -0.57 13 13
STAT3 0.015 0 -10000 0 -10000 0 0
STAT1 0.009 0.053 -10000 0 -0.48 3 3
NFKB1 0.015 0 -10000 0 -10000 0 0
NFKB2 0.015 0 -10000 0 -10000 0 0
IL12B -0.001 0.081 -10000 0 -0.47 7 7
CD8A -0.043 0.18 -10000 0 -0.57 27 27
CD8B -0.036 0.16 -10000 0 -0.56 24 24
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.011 0.12 0.33 15 -10000 0 15
IL2RB 0.004 0.079 -10000 0 -0.57 5 5
proteasomal ubiquitin-dependent protein catabolic process -0.057 0.35 -10000 0 -0.7 46 46
IL2RG -0.012 0.12 -10000 0 -0.53 13 13
IL12 0.007 0.079 -10000 0 -0.33 11 11
STAT5A 0.013 0.036 -10000 0 -0.57 1 1
CD247 -0.001 0.085 -10000 0 -0.56 6 6
IL2 0.005 0.007 -10000 0 -10000 0 0
SPHK2 0.013 0.03 -10000 0 -0.48 1 1
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.008 0.065 -10000 0 -0.49 4 4
IL12/IL12R/TYK2/JAK2 -0.15 0.53 -10000 0 -1.1 48 48
MAP2K3 -0.066 0.37 -10000 0 -0.86 33 33
RIPK2 0.015 0 -10000 0 -10000 0 0
MAP2K6 -0.07 0.37 -10000 0 -0.86 35 35
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.01 0.11 -10000 0 -0.57 10 10
IL18RAP -0.013 0.13 -10000 0 -0.57 14 14
IL12Rbeta1/TYK2 -0.004 0.11 -10000 0 -0.38 18 18
EOMES -0.06 0.3 -10000 0 -1.4 12 12
STAT1 (dimer) -0.079 0.34 -10000 0 -0.72 43 43
T cell proliferation -0.039 0.29 -10000 0 -0.61 38 38
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.012 0.063 -10000 0 -0.58 3 3
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.13 0.24 -10000 0 -0.64 40 40
ATF2 -0.046 0.34 -10000 0 -0.78 33 33
BCR signaling pathway

Figure S45.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S45.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.054 0.16 -9999 0 -0.41 32 32
IKBKB -0.007 0.073 -9999 0 -0.27 3 3
AKT1 -0.049 0.12 -9999 0 -0.24 55 55
IKBKG -0.005 0.076 -9999 0 -0.29 3 3
CALM1 -0.043 0.13 -9999 0 -0.4 19 19
PIK3CA 0.015 0 -9999 0 -10000 0 0
MAP3K1 -0.093 0.24 -9999 0 -0.54 45 45
MAP3K7 0.015 0 -9999 0 -10000 0 0
mol:Ca2+ -0.053 0.14 -9999 0 -0.42 20 20
DOK1 0.013 0.03 -9999 0 -0.48 1 1
AP-1 -0.051 0.11 -9999 0 -0.24 37 37
LYN 0.015 0 -9999 0 -10000 0 0
BLNK -0.002 0.099 -9999 0 -0.57 8 8
SHC1 0.013 0.03 -9999 0 -0.48 1 1
BCR complex -0.095 0.22 -9999 0 -0.46 65 65
CD22 -0.19 0.31 -9999 0 -0.68 60 60
CAMK2G -0.032 0.12 -9999 0 -0.39 16 16
CSNK2A1 0.015 0 -9999 0 -10000 0 0
INPP5D 0.002 0.086 -9999 0 -0.57 6 6
SHC/GRB2/SOS1 -0.074 0.14 -9999 0 -0.48 16 16
GO:0007205 -0.054 0.14 -9999 0 -0.43 20 20
SYK 0.011 0.05 -9999 0 -0.57 2 2
ELK1 -0.043 0.13 -9999 0 -0.41 19 19
NFATC1 -0.1 0.24 -9999 0 -0.51 50 50
B-cell antigen/BCR complex -0.095 0.22 -9999 0 -0.46 65 65
PAG1/CSK 0.022 0 -9999 0 -10000 0 0
NFKBIB 0.009 0.028 -9999 0 -10000 0 0
HRAS -0.038 0.13 -9999 0 -0.38 19 19
NFKBIA 0.009 0.028 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B beta 0.015 0.023 -9999 0 -10000 0 0
RasGAP/Csk -0.067 0.2 -9999 0 -0.56 27 27
mol:GDP -0.051 0.13 -9999 0 -0.4 20 20
PTEN 0.015 0 -9999 0 -10000 0 0
CD79B -0.02 0.14 -9999 0 -0.54 17 17
NF-kappa-B/RelA/I kappa B alpha 0.015 0.023 -9999 0 -10000 0 0
GRB2 0.015 0 -9999 0 -10000 0 0
PI3K/BCAP/CD19 -0.12 0.24 -9999 0 -0.52 56 56
PIK3R1 0.015 0 -9999 0 -10000 0 0
mol:IP3 -0.055 0.14 -9999 0 -0.44 20 20
CSK 0.015 0 -9999 0 -10000 0 0
FOS -0.12 0.18 -9999 0 -0.44 36 36
CHUK -0.005 0.076 -9999 0 -0.29 3 3
IBTK 0.015 0 -9999 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.053 0.11 -9999 0 -0.44 11 11
PTPN6 -0.14 0.3 -9999 0 -0.64 57 57
RELA 0.015 0 -9999 0 -10000 0 0
BCL2A1 0.012 0.032 -9999 0 -0.1 11 11
VAV2 -0.18 0.28 -9999 0 -0.66 52 52
ubiquitin-dependent protein catabolic process 0.014 0.027 -9999 0 -10000 0 0
BTK -0.054 0.25 -9999 0 -1.1 13 13
CD19 -0.19 0.29 -9999 0 -0.67 55 55
MAP4K1 0 0.091 -9999 0 -0.55 7 7
CD72 -0.002 0.09 -9999 0 -0.48 9 9
PAG1 0.015 0 -9999 0 -10000 0 0
MAPK14 -0.069 0.2 -9999 0 -0.45 45 45
SH3BP5 0.013 0.036 -9999 0 -0.57 1 1
PIK3AP1 -0.052 0.16 -9999 0 -0.48 24 24
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.068 0.21 -9999 0 -0.42 56 56
RAF1 -0.029 0.12 -9999 0 -0.49 8 8
RasGAP/p62DOK/SHIP -0.1 0.19 -9999 0 -0.57 28 28
CD79A -0.12 0.24 -9999 0 -0.56 61 61
re-entry into mitotic cell cycle -0.051 0.11 -9999 0 -0.24 37 37
RASA1 0.015 0 -9999 0 -10000 0 0
MAPK3 -0.009 0.1 -9999 0 -0.39 8 8
MAPK1 -0.009 0.1 -9999 0 -0.39 8 8
CD72/SHP1 -0.13 0.28 -9999 0 -0.63 53 53
NFKB1 0.015 0 -9999 0 -10000 0 0
MAPK8 -0.072 0.2 -9999 0 -0.45 46 46
actin cytoskeleton organization -0.12 0.24 -9999 0 -0.55 50 50
NF-kappa-B/RelA 0.035 0.045 -9999 0 -10000 0 0
Calcineurin -0.045 0.096 -9999 0 -0.44 8 8
PI3K -0.16 0.21 -9999 0 -0.49 64 64
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.054 0.15 -9999 0 -0.44 23 23
SOS1 0.015 0 -9999 0 -10000 0 0
Bam32/HPK1 -0.11 0.28 -9999 0 -0.77 34 34
DAPP1 -0.15 0.29 -9999 0 -0.86 33 33
cytokine secretion -0.095 0.21 -9999 0 -0.47 50 50
mol:DAG -0.055 0.14 -9999 0 -0.44 20 20
PLCG2 0.011 0.047 -9999 0 -0.52 2 2
MAP2K1 -0.019 0.12 -9999 0 -0.44 8 8
B-cell antigen/BCR complex/FcgammaRIIB -0.097 0.23 -9999 0 -0.46 70 70
mol:PI-3-4-5-P3 -0.11 0.14 -9999 0 -0.34 63 63
ETS1 -0.021 0.11 -9999 0 -0.44 8 8
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.056 0.18 -9999 0 -0.55 16 16
B-cell antigen/BCR complex/LYN -0.14 0.26 -9999 0 -0.54 61 61
MALT1 0.015 0 -9999 0 -10000 0 0
TRAF6 0.015 0 -9999 0 -10000 0 0
RAC1 -0.13 0.26 -9999 0 -0.6 50 50
B-cell antigen/BCR complex/LYN/SYK -0.17 0.27 -9999 0 -0.63 56 56
CARD11 -0.052 0.14 -9999 0 -0.41 24 24
FCGR2B -0.03 0.15 -9999 0 -0.56 21 21
PPP3CA 0.015 0 -9999 0 -10000 0 0
BCL10 0.015 0 -9999 0 -10000 0 0
IKK complex 0.005 0.038 -9999 0 -0.096 1 1
PTPRC -0.063 0.2 -9999 0 -0.56 36 36
PDPK1 -0.05 0.12 -9999 0 -0.23 53 53
PPP3CB 0.015 0 -9999 0 -10000 0 0
PPP3CC 0.015 0 -9999 0 -10000 0 0
POU2F2 0.016 0.023 -9999 0 -0.1 4 4
S1P4 pathway

Figure S46.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S46.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.16 0.27 -9999 0 -0.57 80 80
CDC42/GTP -0.086 0.18 -9999 0 -0.43 40 40
PLCG1 -0.088 0.18 -9999 0 -0.45 40 40
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.015 0 -9999 0 -10000 0 0
GNAI3 0.015 0 -9999 0 -10000 0 0
G12/G13 0.022 0 -9999 0 -10000 0 0
cell migration -0.11 0.16 -9999 0 -0.42 40 40
S1PR5 -0.008 0.11 -9999 0 -0.5 12 12
S1PR4 0.003 0.08 -9999 0 -0.52 6 6
MAPK3 -0.088 0.18 -9999 0 -0.45 40 40
MAPK1 -0.088 0.18 -9999 0 -0.45 40 40
S1P/S1P5/Gi -0.1 0.2 -9999 0 -0.36 82 82
GNAI1 0.013 0.036 -9999 0 -0.57 1 1
CDC42/GDP 0.011 0 -9999 0 -10000 0 0
S1P/S1P5/G12 0.006 0.065 -9999 0 -0.29 12 12
RHOA 0.029 0.043 -9999 0 -0.28 3 3
S1P/S1P4/Gi -0.1 0.2 -9999 0 -0.36 81 81
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.12 0.24 -9999 0 -0.57 60 60
S1P/S1P4/G12/G13 0.022 0.046 -9999 0 -0.28 6 6
GNA12 0.015 0 -9999 0 -10000 0 0
GNA13 0.015 0 -9999 0 -10000 0 0
CDC42 0.015 0 -9999 0 -10000 0 0
Wnt signaling

Figure S47.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S47.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.037 0.14 -9999 0 -0.3 41 41
FZD6 0.015 0 -9999 0 -10000 0 0
WNT6 -0.057 0.18 -9999 0 -0.51 37 37
WNT4 -0.032 0.16 -9999 0 -0.56 22 22
FZD3 0.011 0.05 -9999 0 -0.57 2 2
WNT5A -0.009 0.11 -9999 0 -0.52 12 12
WNT11 -0.044 0.17 -9999 0 -0.51 30 30
S1P3 pathway

Figure S48.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S48.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.004 0.079 -9999 0 -0.57 5 5
mol:S1P 0.001 0.005 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.099 0.19 -9999 0 -0.39 63 63
GNAO1 -0.16 0.27 -9999 0 -0.57 80 80
S1P/S1P3/G12/G13 0.022 0.053 -9999 0 -0.3 7 7
AKT1 -0.032 0.14 -9999 0 -0.89 5 5
AKT3 -0.065 0.27 -9999 0 -1.3 10 10
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.004 0.079 -9999 0 -0.56 5 5
GNAI2 0.016 0.004 -9999 0 -10000 0 0
GNAI3 0.016 0.004 -9999 0 -10000 0 0
GNAI1 0.014 0.036 -9999 0 -0.56 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.001 0.091 -9999 0 -0.55 7 7
S1PR2 0.015 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.1 0.22 -9999 0 -0.5 48 48
MAPK3 -0.091 0.21 -9999 0 -0.47 48 48
MAPK1 -0.091 0.21 -9999 0 -0.47 48 48
JAK2 -0.091 0.22 -9999 0 -0.48 49 49
CXCR4 -0.095 0.22 -9999 0 -0.48 50 50
FLT1 0.018 0.004 -9999 0 -10000 0 0
RhoA/GDP 0.011 0 -9999 0 -10000 0 0
Rac1/GDP 0.011 0 -9999 0 -10000 0 0
SRC -0.091 0.21 -9999 0 -0.47 48 48
S1P/S1P3/Gi -0.1 0.22 -9999 0 -0.5 48 48
RAC1 0.015 0 -9999 0 -10000 0 0
RhoA/GTP -0.089 0.2 -9999 0 -0.46 48 48
VEGFA 0.018 0.004 -9999 0 -10000 0 0
S1P/S1P2/Gi -0.095 0.19 -9999 0 -0.35 82 82
VEGFR1 homodimer/VEGFA homodimer 0.03 0.009 -9999 0 -10000 0 0
RHOA 0.015 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.02 0.12 -9999 0 -0.25 51 51
GNAQ 0.015 0 -9999 0 -10000 0 0
GNAZ -0.12 0.24 -9999 0 -0.57 60 60
G12/G13 0.022 0 -9999 0 -10000 0 0
GNA14 -0.079 0.21 -9999 0 -0.57 43 43
GNA15 0.011 0.05 -9999 0 -0.57 2 2
GNA12 0.015 0 -9999 0 -10000 0 0
GNA13 0.015 0 -9999 0 -10000 0 0
GNA11 0.013 0.036 -9999 0 -0.57 1 1
Rac1/GTP -0.089 0.2 -9999 0 -0.46 48 48
Coregulation of Androgen receptor activity

Figure S49.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S49.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NRIP1 0.011 0.016 -9999 0 -10000 0 0
SVIL 0.005 0.063 -9999 0 -0.57 3 3
ZNF318 0.026 0.038 -9999 0 -10000 0 0
JMJD2C -0.003 0.027 -9999 0 -0.069 35 35
T-DHT/AR/Ubc9 -0.12 0.19 -9999 0 -0.37 90 90
CARM1 0.015 0.002 -9999 0 -10000 0 0
PRDX1 0.016 0.002 -9999 0 -10000 0 0
PELP1 0.017 0.006 -9999 0 -10000 0 0
CTNNB1 0.012 0.012 -9999 0 -10000 0 0
AKT1 0.018 0.01 -9999 0 -10000 0 0
PTK2B 0.01 0.037 -9999 0 -0.57 1 1
MED1 0.018 0.012 -9999 0 -10000 0 0
MAK 0.013 0.088 -9999 0 -0.47 7 7
response to oxidative stress 0.001 0.003 -9999 0 -10000 0 0
HIP1 0.009 0.038 -9999 0 -0.56 1 1
GSN 0 0.08 -9999 0 -0.57 5 5
NCOA2 -0.02 0.14 -9999 0 -0.57 16 16
NCOA6 0.009 0.033 -9999 0 -0.48 1 1
DNA-PK 0.034 0.04 -9999 0 -10000 0 0
NCOA4 0.015 0.002 -9999 0 -10000 0 0
PIAS3 0.012 0.012 -9999 0 -10000 0 0
cell proliferation -0.017 0.053 -9999 0 -10000 0 0
XRCC5 0.017 0.008 -9999 0 -10000 0 0
UBE3A 0.009 0.023 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.14 0.22 -9999 0 -0.42 96 96
FHL2 -0.017 0.11 -9999 0 -1.2 1 1
RANBP9 0.011 0.014 -9999 0 -10000 0 0
JMJD1A -0.014 0.058 -9999 0 -0.12 53 53
CDK6 -0.006 0.11 -9999 0 -0.57 10 10
TGFB1I1 -0.004 0.095 -9999 0 -0.57 7 7
T-DHT/AR/CyclinD1 -0.13 0.2 -9999 0 -0.38 97 97
XRCC6 0.017 0.008 -9999 0 -10000 0 0
T-DHT/AR -0.12 0.21 -9999 0 -0.38 93 93
CTDSP1 0.014 0.004 -9999 0 -10000 0 0
CTDSP2 0.022 0.025 -9999 0 -10000 0 0
BRCA1 0.009 0.035 -9999 0 -0.51 1 1
TCF4 0.014 0.064 -9999 0 -0.57 3 3
CDKN2A -0.22 0.25 -9999 0 -0.48 127 127
SRF 0.027 0.014 -9999 0 -10000 0 0
NKX3-1 -0.075 0.17 -9999 0 -0.9 5 5
KLK3 -0.078 0.34 -9999 0 -1.5 14 14
TMF1 0.014 0.003 -9999 0 -10000 0 0
HNRNPA1 0.019 0.014 -9999 0 -10000 0 0
AOF2 -0.005 0.017 -9999 0 -0.071 14 14
APPL1 0.032 0.022 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.11 0.19 -9999 0 -0.37 90 90
AR -0.19 0.28 -9999 0 -0.58 90 90
UBA3 0.014 0.004 -9999 0 -10000 0 0
PATZ1 0.019 0.014 -9999 0 -10000 0 0
PAWR 0.012 0.036 -9999 0 -0.57 1 1
PRKDC 0.017 0.008 -9999 0 -10000 0 0
PA2G4 0.02 0.017 -9999 0 -10000 0 0
UBE2I 0.015 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.1 0.17 -9999 0 -0.34 90 90
RPS6KA3 0.011 0.016 -9999 0 -10000 0 0
T-DHT/AR/ARA70 -0.12 0.19 -9999 0 -0.37 90 90
LATS2 0.017 0.038 -9999 0 -0.57 1 1
T-DHT/AR/PRX1 -0.099 0.17 -9999 0 -0.34 90 90
Cyclin D3/CDK11 p58 0.012 0.003 -9999 0 -10000 0 0
VAV3 -0.002 0.086 -9999 0 -0.52 7 7
KLK2 -0.092 0.13 -9999 0 -0.37 35 35
CASP8 0.016 0.005 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.12 0.19 -9999 0 -0.35 98 98
TMPRSS2 -0.22 0.42 -9999 0 -1 52 52
CCND1 -0.01 0.11 -9999 0 -0.51 12 12
PIAS1 0.009 0.023 -9999 0 -10000 0 0
mol:T-DHT -0.009 0.027 -9999 0 -0.071 29 29
CDC2L1 0 0.001 -9999 0 -10000 0 0
PIAS4 0.005 0.036 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.13 0.2 -9999 0 -0.38 96 96
CMTM2 0.012 0.043 -9999 0 -0.48 2 2
SNURF -0.033 0.16 -9999 0 -0.57 21 21
ZMIZ1 0.009 0.023 -9999 0 -10000 0 0
CCND3 0.015 0.001 -9999 0 -10000 0 0
TGIF1 0.019 0.014 -9999 0 -10000 0 0
FKBP4 0.011 0.014 -9999 0 -10000 0 0
Osteopontin-mediated events

Figure S50.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S50.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.083 0.15 -9999 0 -0.54 3 3
NF kappa B1 p50/RelA/I kappa B alpha -0.047 0.14 -9999 0 -0.48 3 3
alphaV/beta3 Integrin/Osteopontin/Src -0.13 0.16 -9999 0 -0.33 108 108
AP1 -0.16 0.24 -9999 0 -0.52 58 58
ILK -0.097 0.15 -9999 0 -0.58 3 3
bone resorption -0.071 0.15 -9999 0 -0.46 12 12
PTK2B 0.013 0.036 -9999 0 -0.57 1 1
PYK2/p130Cas -0.096 0.12 -9999 0 -0.52 3 3
ITGAV 0.016 0.036 -9999 0 -0.57 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.003 0.1 -9999 0 -0.4 16 16
alphaV/beta3 Integrin/Osteopontin -0.14 0.15 -9999 0 -0.33 54 54
MAP3K1 -0.098 0.15 -9999 0 -0.41 8 8
JUN 0 0.093 -9999 0 -0.57 7 7
MAPK3 -0.083 0.15 -9999 0 -0.32 27 27
MAPK1 -0.083 0.15 -9999 0 -0.34 18 18
Rac1/GDP 0.011 0 -9999 0 -10000 0 0
NFKB1 0.015 0 -9999 0 -10000 0 0
MAPK8 -0.086 0.15 -9999 0 -0.47 6 6
ITGB3 -0.045 0.18 -9999 0 -0.56 29 29
NFKBIA -0.067 0.15 -9999 0 -0.54 3 3
FOS -0.16 0.27 -9999 0 -0.57 80 80
CD44 -0.006 0.11 -9999 0 -0.56 10 10
CHUK 0.015 0 -9999 0 -10000 0 0
PLAU -0.082 0.17 -9999 0 -0.48 12 12
NF kappa B1 p50/RelA -0.089 0.099 -9999 0 -0.47 3 3
BCAR1 0.015 0 -9999 0 -10000 0 0
RELA 0.015 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.034 0.13 -9999 0 -0.41 29 29
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.1 0.15 -9999 0 -0.31 31 31
VAV3 -0.091 0.15 -9999 0 -0.48 7 7
MAP3K14 -0.098 0.16 -9999 0 -0.31 32 32
ROCK2 0.002 0.086 -9999 0 -0.57 6 6
SPP1 -0.18 0.24 -9999 0 -0.48 107 107
RAC1 0.015 0 -9999 0 -10000 0 0
Rac1/GTP -0.077 0.14 -9999 0 -0.47 6 6
MMP2 -0.15 0.23 -9999 0 -0.55 44 44
JNK signaling in the CD4+ TCR pathway

Figure S51.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S51.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 -0.014 0.14 -9999 0 -0.34 36 36
MAP4K1 0 0.091 -9999 0 -0.55 7 7
MAP3K8 0.009 0.061 -9999 0 -0.57 3 3
PRKCB -0.15 0.26 -9999 0 -0.57 75 75
DBNL 0.015 0 -9999 0 -10000 0 0
CRKL 0.011 0.043 -9999 0 -0.48 2 2
MAP3K1 0.01 0.11 -9999 0 -0.52 4 4
JUN -0.15 0.29 -9999 0 -0.58 78 78
MAP3K7 0.01 0.11 -9999 0 -0.52 4 4
GRAP2 -0.059 0.19 -9999 0 -0.57 34 34
CRK 0.015 0 -9999 0 -10000 0 0
MAP2K4 0.017 0.11 -9999 0 -0.48 5 5
LAT 0.013 0.03 -9999 0 -0.48 1 1
LCP2 0.013 0.036 -9999 0 -0.57 1 1
MAPK8 -0.15 0.3 -9999 0 -0.61 78 78
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.002 0.12 -9999 0 -0.56 4 4
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.005 0.13 -9999 0 -0.64 4 4
TCGA08_p53

Figure S52.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S52.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2A -0.16 0.18 -10000 0 -0.35 127 127
TP53 -0.038 0.056 -10000 0 -10000 0 0
Senescence -0.038 0.056 -10000 0 -10000 0 0
Apoptosis -0.038 0.056 -10000 0 -10000 0 0
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.073 0.11 0.26 4 -0.31 8 12
MDM4 0.015 0 -10000 0 -10000 0 0
Arf6 signaling events

Figure S53.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S53.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.015 0.044 -9999 0 -0.35 4 4
ARNO/beta Arrestin1-2 -0.023 0.071 -9999 0 -0.36 1 1
EGFR -0.007 0.11 -9999 0 -0.52 11 11
EPHA2 0.011 0.05 -9999 0 -0.57 2 2
USP6 0.015 0 -9999 0 -10000 0 0
IQSEC1 0.013 0.03 -9999 0 -0.48 1 1
EGFR/EGFR/EGF/EGF -0.015 0.11 -9999 0 -0.35 26 26
ARRB2 0.011 0.016 -9999 0 -0.17 2 2
mol:GTP 0.014 0.035 -9999 0 -0.21 4 4
ARRB1 0.011 0.05 -9999 0 -0.57 2 2
FBXO8 0.015 0 -9999 0 -10000 0 0
TSHR 0.002 0.067 -9999 0 -0.48 5 5
EGF -0.014 0.11 -9999 0 -0.48 15 15
somatostatin receptor activity 0 0 -9999 0 -0.001 47 47
ARAP2 0.011 0.05 -9999 0 -0.57 2 2
mol:GDP -0.069 0.11 -9999 0 -0.24 61 61
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 31 31
ITGA2B -0.024 0.13 -9999 0 -0.48 21 21
ARF6 0.015 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.029 0.053 -9999 0 -0.3 2 2
ADAP1 0.006 0.071 -9999 0 -0.57 4 4
KIF13B 0.015 0 -9999 0 -10000 0 0
HGF/MET -0.082 0.18 -9999 0 -0.4 66 66
PXN 0.015 0 -9999 0 -10000 0 0
ARF6/GTP -0.064 0.12 -9999 0 -0.26 47 47
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.002 0.095 -9999 0 -0.29 27 27
ADRB2 -0.033 0.16 -9999 0 -0.57 22 22
receptor agonist activity 0 0 -9999 0 0 54 54
actin filament binding 0 0 -9999 0 0 47 47
SRC 0.015 0 -9999 0 -10000 0 0
ITGB3 -0.048 0.18 -9999 0 -0.57 29 29
GNAQ 0.015 0 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 40 40
ARF6/GDP 0.007 0.097 -9999 0 -0.37 12 12
ARF6/GDP/GULP/ACAP1 -0.11 0.17 -9999 0 -0.41 51 51
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.019 0.13 -9999 0 -0.33 29 29
ACAP1 -0.014 0.13 -9999 0 -0.55 14 14
ACAP2 0.015 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 0.003 0.023 -9999 0 -0.25 2 2
EFNA1 0.002 0.08 -9999 0 -0.48 7 7
HGF -0.13 0.25 -9999 0 -0.56 66 66
CYTH3 0.013 0 -9999 0 -10000 0 0
CYTH2 0.01 0.002 -9999 0 -10000 0 0
NCK1 0.015 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 36 36
endosomal lumen acidification 0 0 0 2 0 49 51
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.072 0.21 -9999 0 -0.57 40 40
GNAQ/ARNO 0.017 0.007 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 3 3
MET 0.015 0 -9999 0 -10000 0 0
GNA14 -0.079 0.21 -9999 0 -0.57 43 43
GNA15 0.011 0.05 -9999 0 -0.57 2 2
GIT1 0.015 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 43 43
GNA11 0.013 0.036 -9999 0 -0.57 1 1
LHCGR 0 0.043 -9999 0 -0.48 2 2
AGTR1 -0.24 0.29 -9999 0 -0.57 116 116
desensitization of G-protein coupled receptor protein signaling pathway 0.003 0.023 -9999 0 -0.25 2 2
IPCEF1/ARNO -0.001 0.072 -9999 0 -10000 0 0
alphaIIb/beta3 Integrin -0.051 0.17 -9999 0 -0.4 46 46
Aurora A signaling

Figure S54.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S54.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A -0.017 0.073 -9999 0 -10000 0 0
BIRC5 -0.35 0.22 -9999 0 -0.48 197 197
NFKBIA -0.016 0.074 -9999 0 -10000 0 0
CPEB1 -0.27 0.29 -9999 0 -0.57 128 128
AKT1 -0.016 0.074 -9999 0 -10000 0 0
NDEL1 0.015 0 -9999 0 -10000 0 0
Aurora A/BRCA1 -0.023 0.065 -9999 0 -0.38 1 1
NDEL1/TACC3 -0.024 0.095 -9999 0 -0.35 9 9
GADD45A 0.015 0 -9999 0 -10000 0 0
GSK3B 0.017 0.003 -9999 0 -10000 0 0
PAK1/Aurora A -0.019 0.078 -9999 0 -0.46 1 1
MDM2 0 0.085 -9999 0 -0.48 8 8
JUB 0.011 0.043 -9999 0 -0.48 2 2
TPX2 -0.18 0.18 -9999 0 -0.34 148 148
TP53 -0.001 0.052 -9999 0 -10000 0 0
DLG7 -0.027 0.073 -9999 0 -10000 0 0
AURKAIP1 0.013 0.03 -9999 0 -0.48 1 1
ARHGEF7 0.015 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 -0.026 0.1 -9999 0 -0.37 9 9
G2/M transition of mitotic cell cycle -0.023 0.065 -9999 0 -0.37 1 1
AURKA -0.031 0.091 -9999 0 -10000 0 0
AURKB -0.04 0.052 -9999 0 -10000 0 0
CDC25B -0.01 0.067 -9999 0 -0.22 6 6
G2/M transition checkpoint -0.024 0.066 -9999 0 -0.31 2 2
mRNA polyadenylation -0.18 0.18 -9999 0 -0.36 128 128
Aurora A/CPEB -0.18 0.18 -9999 0 -0.36 128 128
Aurora A/TACC1/TRAP/chTOG 0.004 0.066 -9999 0 -0.39 1 1
BRCA1 0.013 0.03 -9999 0 -0.48 1 1
centrosome duplication -0.019 0.077 -9999 0 -0.46 1 1
regulation of centrosome cycle -0.033 0.089 -9999 0 -0.34 9 9
spindle assembly 0.003 0.065 -9999 0 -0.39 1 1
TDRD7 0.015 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.19 0.13 -9999 0 -0.33 83 83
CENPA -0.04 0.053 -9999 0 -10000 0 0
Aurora A/PP2A -0.017 0.073 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.002 0.056 -9999 0 -10000 0 0
negative regulation of DNA binding -0.001 0.052 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0.022 0 -9999 0 -10000 0 0
RASA1 0.015 0 -9999 0 -10000 0 0
Ajuba/Aurora A -0.024 0.066 -9999 0 -0.31 2 2
mitotic prometaphase 0.011 0.014 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.031 0.091 -9999 0 -10000 0 0
TACC1 0.013 0.036 -9999 0 -0.57 1 1
TACC3 -0.022 0.13 -9999 0 -0.48 20 20
Aurora A/Antizyme1 -0.006 0.067 -9999 0 -10000 0 0
Aurora A/RasGAP -0.017 0.073 -9999 0 -10000 0 0
OAZ1 0.015 0 -9999 0 -10000 0 0
RAN 0.015 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.017 0.003 -9999 0 -10000 0 0
GIT1 0.015 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.029 0.022 -9999 0 -0.34 1 1
Importin alpha/Importin beta/TPX2 -0.18 0.18 -9999 0 -0.34 148 148
PPP2R5D 0.015 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.16 0.18 -9999 0 -0.36 83 83
PAK1 0.013 0.036 -9999 0 -0.57 1 1
CKAP5 0.015 0 -9999 0 -10000 0 0
Class IB PI3K non-lipid kinase events

Figure S55.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S55.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process 0.024 0.14 0.56 18 -10000 0 18
PI3K Class IB/PDE3B -0.024 0.15 -10000 0 -0.56 18 18
PDE3B -0.024 0.15 -10000 0 -0.57 18 18
Syndecan-2-mediated signaling events

Figure S56.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S56.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.02 0.12 -9999 0 -0.32 37 37
EPHB2 -0.015 0.12 -9999 0 -0.48 16 16
Syndecan-2/TACI -0.028 0.13 -9999 0 -0.34 39 39
LAMA1 -0.083 0.2 -9999 0 -0.5 51 51
Syndecan-2/alpha2 ITGB1 -0.031 0.14 -9999 0 -0.32 36 36
HRAS 0.015 0 -9999 0 -10000 0 0
Syndecan-2/CASK -0.002 0.08 -9999 0 -0.34 14 14
ITGA5 -0.004 0.1 -9999 0 -0.57 9 9
BAX 0.024 0.08 -9999 0 -10000 0 0
EPB41 0.015 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion 0.008 0.073 -9999 0 -0.3 14 14
LAMA3 -0.086 0.21 -9999 0 -0.53 50 50
EZR 0.015 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.009 0.061 -9999 0 -0.57 3 3
Syndecan-2/MMP2 -0.024 0.15 -9999 0 -0.42 31 31
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 0.017 0.046 -9999 0 -0.35 4 4
dendrite morphogenesis -0.009 0.1 -9999 0 -0.3 30 30
Syndecan-2/GM-CSF -0.046 0.13 -9999 0 -0.29 61 61
determination of left/right symmetry 0 0.095 -9999 0 -0.4 14 14
Syndecan-2/PKC delta 0.009 0.081 -9999 0 -0.34 14 14
GNB2L1 0.015 0 -9999 0 -10000 0 0
MAPK3 -0.031 0.12 -9999 0 -0.25 61 61
MAPK1 -0.031 0.12 -9999 0 -0.3 14 14
Syndecan-2/RACK1 0.018 0.07 -9999 0 -0.28 14 14
NF1 0.015 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0 0.095 -9999 0 -0.4 14 14
ITGA2 0.007 0.063 -9999 0 -0.5 4 4
MAPK8 0.015 0.09 -9999 0 -0.33 17 17
Syndecan-2/alpha2/beta1 Integrin -0.029 0.13 -9999 0 -0.32 24 24
Syndecan-2/Kininogen -0.002 0.08 -9999 0 -0.34 14 14
ITGB1 0.015 0 -9999 0 -10000 0 0
SRC 0.025 0.066 -9999 0 -0.26 14 14
Syndecan-2/CASK/Protein 4.1 0.008 0.074 -9999 0 -0.3 14 14
extracellular matrix organization 0.009 0.081 -9999 0 -0.33 14 14
actin cytoskeleton reorganization -0.02 0.12 -9999 0 -0.32 37 37
Syndecan-2/Caveolin-2/Ras 0.015 0.085 -9999 0 -0.32 16 16
Syndecan-2/Laminin alpha3 -0.053 0.16 -9999 0 -0.34 59 59
Syndecan-2/RasGAP 0.025 0.067 -9999 0 -10000 0 0
alpha5/beta1 Integrin 0.008 0.077 -9999 0 -0.41 9 9
PRKCD 0.015 0 -9999 0 -10000 0 0
Syndecan-2 dimer -0.009 0.1 -9999 0 -0.3 30 30
GO:0007205 0.004 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.034 0.065 -9999 0 -10000 0 0
RHOA 0.015 0 -9999 0 -10000 0 0
SDCBP 0.015 0 -9999 0 -10000 0 0
TNFRSF13B -0.044 0.17 -9999 0 -0.55 26 26
RASA1 0.015 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin 0.017 0.046 -9999 0 -0.35 4 4
Syndecan-2/Synbindin 0.009 0.081 -9999 0 -0.34 14 14
TGFB1 0.015 0 -9999 0 -10000 0 0
CASP3 0.019 0.074 -9999 0 -0.3 14 14
FN1 -0.032 0.15 -9999 0 -0.51 24 24
Syndecan-2/IL8 -0.046 0.16 -9999 0 -0.36 51 51
SDC2 0 0.095 -9999 0 -0.4 14 14
KNG1 0 0 -9999 0 -10000 0 0
Syndecan-2/Neurofibromin 0.009 0.081 -9999 0 -0.34 14 14
TRAPPC4 0.015 0 -9999 0 -10000 0 0
CSF2 -0.074 0.19 -9999 0 -0.48 47 47
Syndecan-2/TGFB1 0.009 0.081 -9999 0 -0.34 14 14
Syndecan-2/Syntenin/PI-4-5-P2 0.008 0.074 -9999 0 -0.3 14 14
Syndecan-2/Ezrin 0.019 0.074 -9999 0 -0.3 14 14
PRKACA 0.019 0.074 -9999 0 -0.3 14 14
angiogenesis -0.046 0.16 -9999 0 -0.36 51 51
MMP2 -0.039 0.17 -9999 0 -0.57 25 25
IL8 -0.074 0.21 -9999 0 -0.56 41 41
calcineurin-NFAT signaling pathway -0.028 0.13 -9999 0 -0.34 39 39
Nephrin/Neph1 signaling in the kidney podocyte

Figure S57.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S57.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
positive regulation of NF-kappaB transcription factor activity 0.039 0.14 0.41 33 -10000 0 33
KIRREL -0.047 0.18 -10000 0 -0.58 27 27
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.039 0.14 -10000 0 -0.41 33 33
PLCG1 0.015 0 -10000 0 -10000 0 0
ARRB2 0.015 0 -10000 0 -10000 0 0
WASL 0.015 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.046 0.11 -10000 0 -0.33 27 27
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.005 0.098 -10000 0 -0.29 17 17
FYN -0.027 0.12 -10000 0 -0.33 28 28
mol:Ca2+ -0.045 0.11 -10000 0 -0.33 27 27
mol:DAG -0.046 0.11 -10000 0 -0.33 27 27
NPHS2 -0.021 0.1 -10000 0 -0.49 12 12
mol:IP3 -0.046 0.11 -10000 0 -0.33 27 27
regulation of endocytosis -0.017 0.11 -10000 0 -0.36 12 12
Nephrin/NEPH1/podocin/Cholesterol -0.037 0.12 -10000 0 -0.3 42 42
establishment of cell polarity -0.039 0.14 -10000 0 -0.41 33 33
Nephrin/NEPH1/podocin/NCK1-2 -0.011 0.11 -10000 0 -0.43 5 5
Nephrin/NEPH1/beta Arrestin2 -0.016 0.11 -10000 0 -0.36 12 12
NPHS1 -0.011 0.073 -10000 0 -0.48 6 6
Nephrin/NEPH1/podocin -0.027 0.12 -10000 0 -0.33 28 28
TJP1 0.015 0 -10000 0 -10000 0 0
NCK1 0.015 0 -10000 0 -10000 0 0
NCK2 0.015 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.046 0.11 -10000 0 -0.33 27 27
CD2AP 0.015 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.046 0.11 -10000 0 -0.33 27 27
GRB2 0.015 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.022 0.11 -10000 0 -0.31 27 27
cytoskeleton organization -0.004 0.11 -10000 0 -0.36 12 12
Nephrin/NEPH1 -0.025 0.1 -10000 0 -0.29 33 33
Nephrin/NEPH1/ZO-1 -0.04 0.1 -10000 0 -0.33 27 27
FAS signaling pathway (CD95)

Figure S58.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S58.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPTAN1 0.013 0.053 0.23 14 -10000 0 14
RFC1 0.013 0.053 0.23 14 -10000 0 14
PRKDC 0.013 0.053 0.23 15 -10000 0 15
RIPK1 0.019 0.005 -10000 0 -10000 0 0
CASP7 -0.029 0.045 0.25 2 -10000 0 2
FASLG/FAS/FADD/FAF1 -0.038 0.085 0.22 3 -0.31 16 19
MAP2K4 -0.089 0.17 -10000 0 -0.43 16 16
mol:ceramide -0.057 0.13 -10000 0 -0.39 21 21
GSN 0.007 0.068 0.24 13 -0.34 4 17
FASLG/FAS/FADD/FAF1/Caspase 8 -0.036 0.1 -10000 0 -0.36 16 16
FAS 0 0.071 -10000 0 -0.57 4 4
BID 0.003 0.037 0.3 3 -0.3 1 4
MAP3K1 -0.037 0.1 0.21 2 -0.26 11 13
MAP3K7 0.009 0.007 -10000 0 -10000 0 0
RB1 0.013 0.053 0.23 14 -10000 0 14
CFLAR 0.019 0.005 -10000 0 -10000 0 0
HGF/MET -0.067 0.17 -10000 0 -0.34 70 70
ARHGDIB 0.013 0.053 0.23 15 -10000 0 15
FADD -0.001 0.069 -10000 0 -0.49 5 5
actin filament polymerization -0.007 0.068 0.33 4 -0.24 13 17
NFKB1 -0.096 0.1 -10000 0 -10000 0 0
MAPK8 -0.16 0.25 -10000 0 -0.43 121 121
DFFA 0.013 0.053 0.23 15 -10000 0 15
DNA fragmentation during apoptosis 0.013 0.053 0.24 12 -10000 0 12
FAS/FADD/MET 0.007 0.062 -10000 0 -0.34 6 6
CFLAR/RIP1 0.012 0.011 -10000 0 -10000 0 0
FAIM3 0.009 0.069 -10000 0 -0.55 4 4
FAF1 0.009 0.008 -10000 0 -10000 0 0
PARP1 0.013 0.053 0.24 12 -10000 0 12
DFFB 0.013 0.053 0.24 12 -10000 0 12
CHUK -0.083 0.09 -10000 0 -10000 0 0
FASLG -0.037 0.15 -10000 0 -0.56 21 21
FAS/FADD -0.001 0.073 -10000 0 -0.38 9 9
HGF -0.13 0.25 -10000 0 -0.56 66 66
LMNA 0.012 0.049 0.22 12 -10000 0 12
CASP6 0.013 0.053 0.23 15 -10000 0 15
CASP10 0.009 0.008 -10000 0 -10000 0 0
CASP3 0.015 0.063 0.27 15 -10000 0 15
PTPN13 0.002 0.086 -10000 0 -0.57 6 6
CASP8 0.005 0.043 0.39 3 -10000 0 3
IL6 -0.57 0.67 -10000 0 -1.3 121 121
MET 0.015 0 -10000 0 -10000 0 0
ICAD/CAD 0.012 0.05 0.22 12 -10000 0 12
FASLG/FAS/FADD/FAF1/Caspase 10 -0.058 0.14 -10000 0 -0.39 21 21
activation of caspase activity by cytochrome c 0.003 0.037 0.3 3 -0.3 1 4
PAK2 0.013 0.053 0.23 14 -10000 0 14
BCL2 -0.01 0.12 -10000 0 -0.56 12 12
Angiopoietin receptor Tie2-mediated signaling

Figure S59.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S59.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.039 0.25 -10000 0 -0.83 20 20
NCK1/PAK1/Dok-R -0.035 0.11 -10000 0 -0.41 20 20
NCK1/Dok-R -0.001 0.3 -10000 0 -1 20 20
PIK3CA 0.015 0.001 -10000 0 -10000 0 0
mol:beta2-estradiol 0.002 0.061 0.24 16 -10000 0 16
RELA 0.015 0 -10000 0 -10000 0 0
SHC1 0.014 0.03 -10000 0 -0.48 1 1
Rac/GDP 0.011 0 -10000 0 -10000 0 0
F2 -0.029 0.15 0.25 15 -0.51 20 35
TNIP2 0.015 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.07 0.25 -10000 0 -0.95 20 20
FN1 -0.032 0.15 -10000 0 -0.51 24 24
PLD2 0.003 0.3 -10000 0 -1.1 20 20
PTPN11 0.015 0 -10000 0 -10000 0 0
GRB14 -0.047 0.16 -10000 0 -0.48 33 33
ELK1 0.018 0.28 -10000 0 -0.94 20 20
GRB7 -0.008 0.11 -10000 0 -0.5 12 12
PAK1 0.013 0.036 -10000 0 -0.57 1 1
Tie2/Ang1/alpha5/beta1 Integrin -0.094 0.28 -10000 0 -1.1 20 20
CDKN1A 0.036 0.19 -10000 0 -0.58 18 18
ITGA5 -0.004 0.1 -10000 0 -0.57 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.001 0.3 -10000 0 -1 20 20
CRK 0.015 0 -10000 0 -10000 0 0
mol:NO 0.054 0.2 -10000 0 -0.62 20 20
PLG -0.006 0.3 -10000 0 -1.1 20 20
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.021 0.24 -10000 0 -0.82 20 20
GRB2 0.015 0 -10000 0 -10000 0 0
PIK3R1 0.016 0.001 -10000 0 -10000 0 0
ANGPT2 -0.037 0.19 -10000 0 -0.65 13 13
BMX -0.088 0.34 -10000 0 -1.2 20 20
ANGPT1 -0.029 0.32 -10000 0 -1.3 16 16
tube development 0.028 0.2 -10000 0 -0.64 19 19
ANGPT4 0.003 0.06 -10000 0 -0.48 4 4
response to hypoxia 0.001 0.019 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.03 0.32 -10000 0 -1.1 20 20
alpha5/beta1 Integrin 0.008 0.077 -10000 0 -0.41 9 9
FGF2 -0.18 0.27 -10000 0 -0.57 87 87
STAT5A (dimer) 0.031 0.23 -10000 0 -0.71 19 19
mol:L-citrulline 0.054 0.2 -10000 0 -0.62 20 20
AGTR1 -0.24 0.29 -10000 0 -0.56 116 116
MAPK14 0.003 0.3 -10000 0 -1 20 20
Tie2/SHP2 -0.031 0.16 -10000 0 -1.1 5 5
TEK 0.02 0.19 -10000 0 -1.2 5 5
RPS6KB1 0.036 0.25 -10000 0 -0.81 20 20
Angiotensin II/AT1 -0.17 0.21 -10000 0 -0.41 116 116
Tie2/Ang1/GRB2 -0.001 0.31 -10000 0 -1.1 20 20
MAPK3 0.013 0.28 -10000 0 -0.97 20 20
MAPK1 0.013 0.28 -10000 0 -0.97 20 20
Tie2/Ang1/GRB7 -0.012 0.31 -10000 0 -1.1 20 20
NFKB1 0.015 0 -10000 0 -10000 0 0
MAPK8 -0.001 0.3 -10000 0 -1.1 20 20
PI3K 0.021 0.28 -10000 0 -0.96 20 20
FES 0.002 0.3 -10000 0 -1 20 20
Crk/Dok-R -0.001 0.3 -10000 0 -1 20 20
Tie2/Ang1/ABIN2 -0.001 0.31 -10000 0 -1.1 20 20
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.044 0.23 -10000 0 -0.75 20 20
STAT5A 0.013 0.036 -10000 0 -0.57 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.036 0.25 -10000 0 -0.81 20 20
Tie2/Ang2 0.012 0.26 -10000 0 -0.84 19 19
Tie2/Ang1 -0.007 0.33 -10000 0 -1.1 20 20
FOXO1 0.052 0.23 -10000 0 -0.74 20 20
ELF1 0.024 0.015 -10000 0 -10000 0 0
ELF2 0 0.3 -10000 0 -1 20 20
mol:Choline 0.006 0.29 -10000 0 -1 20 20
cell migration -0.024 0.064 -10000 0 -0.23 21 21
FYN 0.023 0.23 -10000 0 -0.72 19 19
DOK2 -0.006 0.11 -10000 0 -0.56 10 10
negative regulation of cell cycle 0.039 0.18 -10000 0 -0.53 19 19
ETS1 0.012 0.058 -10000 0 -0.24 1 1
PXN 0.049 0.21 -10000 0 -0.67 20 20
ITGB1 0.015 0 -10000 0 -10000 0 0
NOS3 0.051 0.22 -10000 0 -0.7 20 20
RAC1 0.015 0 -10000 0 -10000 0 0
TNF -0.011 0.12 -10000 0 -0.4 19 19
MAPKKK cascade 0.006 0.29 -10000 0 -1 20 20
RASA1 0.015 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.001 0.31 -10000 0 -1.1 20 20
NCK1 0.015 0 -10000 0 -10000 0 0
vasculogenesis 0.057 0.18 -10000 0 -0.55 20 20
mol:Phosphatidic acid 0.006 0.29 -10000 0 -1 20 20
mol:Angiotensin II 0.002 0.001 -10000 0 -10000 0 0
mol:NADP 0.054 0.2 -10000 0 -0.62 20 20
Rac1/GTP -0.058 0.2 -10000 0 -0.75 20 20
MMP2 -0.025 0.33 -10000 0 -1.1 20 20
Presenilin action in Notch and Wnt signaling

Figure S60.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S60.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.005 0.033 -10000 0 -10000 0 0
HDAC1 0.013 0.011 -10000 0 -10000 0 0
AES 0.015 0.004 -10000 0 -10000 0 0
FBXW11 0.015 0 -10000 0 -10000 0 0
DTX1 -0.006 0.11 -10000 0 -0.54 10 10
LRP6/FZD1 0.023 0 -10000 0 -10000 0 0
TLE1 0.01 0.05 -10000 0 -0.57 2 2
AP1 -0.082 0.16 -10000 0 -0.3 89 89
NCSTN 0.015 0 -10000 0 -10000 0 0
ADAM10 0.015 0 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.031 0.072 -10000 0 -0.29 2 2
NICD/RBPSUH 0.038 0.006 -10000 0 -10000 0 0
WIF1 -0.13 0.24 -10000 0 -0.56 64 64
NOTCH1 0 0 -10000 0 -10000 0 0
PSENEN 0.015 0 -10000 0 -10000 0 0
KREMEN2 -0.18 0.24 -10000 0 -0.48 105 105
DKK1 -0.07 0.2 -10000 0 -0.55 40 40
beta catenin/beta TrCP1 0.03 0.043 -10000 0 -10000 0 0
APH1B 0.015 0 -10000 0 -10000 0 0
APH1A 0.015 0 -10000 0 -10000 0 0
AXIN1 0.005 0.014 -10000 0 -10000 0 0
CtBP/CBP/TCF1/TLE1/AES 0.029 0.05 0.27 3 -0.26 2 5
PSEN1 0.015 0 -10000 0 -10000 0 0
FOS -0.16 0.27 -10000 0 -0.57 80 80
JUN 0 0.093 -10000 0 -0.57 7 7
MAP3K7 0.014 0.005 -10000 0 -10000 0 0
CTNNB1 0.022 0.045 0.2 7 -10000 0 7
MAPK3 0.015 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.16 0.2 -10000 0 -0.33 140 140
HNF1A 0.007 0.061 -10000 0 -0.48 4 4
CTBP1 0.013 0.03 -10000 0 -0.48 1 1
MYC -0.044 0.32 -10000 0 -1.4 13 13
NKD1 -0.017 0.13 -10000 0 -0.54 15 15
FZD1 0.015 0 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.027 0.055 -10000 0 -10000 0 0
apoptosis -0.081 0.16 -10000 0 -0.3 89 89
Delta 1/NOTCHprecursor 0.033 0.039 -10000 0 -10000 0 0
DLL1 0.005 0.075 -10000 0 -0.53 5 5
PPARD 0.022 0.026 -10000 0 -10000 0 0
Gamma Secretase 0.043 0.011 -10000 0 -10000 0 0
APC 0.005 0.014 -10000 0 -10000 0 0
DVL1 0.009 0.031 -10000 0 -10000 0 0
CSNK2A1 0.015 0.002 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.005 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.14 0.19 -10000 0 -0.32 128 128
LRP6 0.015 0 -10000 0 -10000 0 0
CSNK1A1 0.015 0.002 -10000 0 -10000 0 0
NLK 0.017 0.012 -10000 0 -10000 0 0
CCND1 -0.007 0.19 -10000 0 -1.5 4 4
WNT1 0.01 0.031 -10000 0 -0.48 1 1
Axin1/APC/beta catenin 0.041 0.032 -10000 0 -10000 0 0
DKK2 -0.1 0.21 -10000 0 -0.48 63 63
NOTCH1 precursor/DVL1 0.001 0.009 -10000 0 -10000 0 0
GSK3B 0.015 0.001 -10000 0 -10000 0 0
FRAT1 0.015 0.002 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.009 0.048 -10000 0 -10000 0 0
PPP2R5D 0.01 0.064 0.27 15 -10000 0 15
MAPK1 0.015 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.049 0.14 -10000 0 -0.3 58 58
RBPJ 0.015 0 -10000 0 -10000 0 0
CREBBP 0.018 0.005 -10000 0 -10000 0 0
Syndecan-4-mediated signaling events

Figure S61.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S61.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.002 0.1 -9999 0 -0.53 8 8
Syndecan-4/Syndesmos -0.027 0.12 -9999 0 -0.51 8 8
positive regulation of JNK cascade -0.1 0.17 -9999 0 -0.51 21 21
Syndecan-4/ADAM12 -0.052 0.15 -9999 0 -0.51 12 12
CCL5 -0.018 0.13 -9999 0 -0.54 16 16
Rac1/GDP 0.011 0 -9999 0 -10000 0 0
DNM2 0.015 0 -9999 0 -10000 0 0
ITGA5 -0.004 0.1 -9999 0 -0.57 9 9
SDCBP 0.015 0 -9999 0 -10000 0 0
PLG 0 0.043 -9999 0 -0.49 2 2
ADAM12 -0.037 0.15 -9999 0 -0.48 28 28
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.015 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.038 0.05 -9999 0 -0.16 1 1
Syndecan-4/Laminin alpha1 -0.074 0.17 -9999 0 -0.55 16 16
Syndecan-4/CXCL12/CXCR4 -0.11 0.18 -9999 0 -0.54 21 21
Syndecan-4/Laminin alpha3 -0.076 0.16 -9999 0 -0.46 20 20
MDK -0.017 0.12 -9999 0 -0.48 17 17
Syndecan-4/FZD7 -0.041 0.13 -9999 0 -0.45 13 13
Syndecan-4/Midkine -0.042 0.13 -9999 0 -0.54 8 8
FZD7 -0.013 0.12 -9999 0 -0.57 13 13
Syndecan-4/FGFR1/FGF -0.18 0.22 -9999 0 -0.55 57 57
THBS1 -0.007 0.11 -9999 0 -0.57 10 10
integrin-mediated signaling pathway -0.056 0.16 -9999 0 -0.5 18 18
positive regulation of MAPKKK cascade -0.1 0.17 -9999 0 -0.51 21 21
Syndecan-4/TACI -0.057 0.14 -9999 0 -0.46 13 13
CXCR4 0.006 0.071 -9999 0 -0.57 4 4
cell adhesion 0.007 0.098 -9999 0 -0.44 9 9
Syndecan-4/Dynamin -0.027 0.12 -9999 0 -0.51 8 8
Syndecan-4/TSP1 -0.038 0.14 -9999 0 -0.53 10 10
Syndecan-4/GIPC -0.027 0.12 -9999 0 -0.51 8 8
Syndecan-4/RANTES -0.043 0.15 -9999 0 -0.6 10 10
ITGB1 0.015 0 -9999 0 -10000 0 0
LAMA1 -0.083 0.2 -9999 0 -0.5 51 51
LAMA3 -0.086 0.21 -9999 0 -0.53 50 50
RAC1 0.015 0 -9999 0 -10000 0 0
PRKCA 0.022 0.047 -9999 0 -0.54 1 1
Syndecan-4/alpha-Actinin -0.027 0.12 -9999 0 -0.51 8 8
TFPI 0 0.093 -9999 0 -0.57 7 7
F2 -0.032 0.13 -9999 0 -0.49 21 21
alpha5/beta1 Integrin 0.008 0.077 -9999 0 -0.41 9 9
positive regulation of cell adhesion -0.11 0.19 -9999 0 -0.54 22 22
ACTN1 0.015 0 -9999 0 -10000 0 0
TNC -0.048 0.18 -9999 0 -0.55 30 30
Syndecan-4/CXCL12 -0.12 0.18 -9999 0 -0.49 29 29
FGF6 0 0.002 -9999 0 -10000 0 0
RHOA 0.015 0 -9999 0 -10000 0 0
CXCL12 -0.17 0.27 -9999 0 -0.57 84 84
TNFRSF13B -0.044 0.17 -9999 0 -0.55 26 26
FGF2 -0.17 0.27 -9999 0 -0.57 87 87
FGFR1 -0.12 0.25 -9999 0 -0.57 63 63
Syndecan-4/PI-4-5-P2 -0.036 0.12 -9999 0 -0.52 8 8
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.031 0.15 -9999 0 -0.51 24 24
cell migration -0.015 0.022 -9999 0 -10000 0 0
PRKCD 0.016 0.007 -9999 0 -10000 0 0
vasculogenesis -0.037 0.13 -9999 0 -0.51 10 10
SDC4 -0.038 0.13 -9999 0 -0.55 8 8
Syndecan-4/Tenascin C -0.058 0.17 -9999 0 -0.52 18 18
Syndecan-4/PI-4-5-P2/PKC alpha -0.03 0.04 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.027 0.12 -9999 0 -0.51 8 8
MMP9 -0.13 0.23 -9999 0 -0.49 77 77
Rac1/GTP 0.006 0.1 -9999 0 -0.46 9 9
cytoskeleton organization -0.026 0.12 -9999 0 -0.49 8 8
GIPC1 0.015 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.034 0.14 -9999 0 -0.6 9 9
Noncanonical Wnt signaling pathway

Figure S62.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S62.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.086 0.22 -9999 0 -0.57 46 46
GNB1/GNG2 -0.02 0.13 -9999 0 -0.5 9 9
mol:DAG -0.01 0.12 -9999 0 -0.46 9 9
PLCG1 -0.01 0.13 -9999 0 -0.47 9 9
YES1 -0.026 0.13 -9999 0 -0.5 9 9
FZD3 0.011 0.05 -9999 0 -0.57 2 2
FZD6 0.015 0 -9999 0 -10000 0 0
G protein -0.011 0.13 -9999 0 -0.48 9 9
MAP3K7 -0.078 0.16 -9999 0 -0.37 36 36
mol:Ca2+ -0.009 0.12 -9999 0 -0.44 9 9
mol:IP3 -0.01 0.12 -9999 0 -0.46 9 9
NLK -0.003 0.008 -9999 0 -10000 0 0
GNB1 0.015 0 -9999 0 -10000 0 0
CAMK2A -0.092 0.18 -9999 0 -0.41 37 37
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.037 0.14 -9999 0 -0.3 41 41
CSNK1A1 0.015 0 -9999 0 -10000 0 0
GNAS -0.026 0.13 -9999 0 -0.5 9 9
GO:0007205 -0.009 0.12 -9999 0 -0.45 9 9
WNT6 -0.057 0.18 -9999 0 -0.51 37 37
WNT4 -0.032 0.16 -9999 0 -0.56 22 22
NFAT1/CK1 alpha -0.051 0.16 -9999 0 -0.46 17 17
GNG2 0.009 0.061 -9999 0 -0.57 3 3
WNT5A -0.009 0.11 -9999 0 -0.52 12 12
WNT11 -0.044 0.17 -9999 0 -0.51 30 30
CDC42 -0.016 0.13 -9999 0 -0.47 9 9
Canonical Wnt signaling pathway

Figure S63.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S63.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.013 0.033 -10000 0 -10000 0 0
AES 0.019 0.025 -10000 0 -10000 0 0
FBXW11 0.015 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.02 0.008 -10000 0 -10000 0 0
SMAD4 0.015 0 -10000 0 -10000 0 0
DKK2 -0.1 0.21 -10000 0 -0.48 63 63
TLE1 0.014 0.056 -10000 0 -0.57 2 2
MACF1 0.015 0 -10000 0 -10000 0 0
CTNNB1 0.042 0.08 0.25 7 -10000 0 7
WIF1 -0.13 0.24 -10000 0 -0.56 64 64
beta catenin/RanBP3 0.036 0.13 0.38 31 -10000 0 31
KREMEN2 -0.18 0.24 -10000 0 -0.48 105 105
DKK1 -0.07 0.2 -10000 0 -0.55 40 40
beta catenin/beta TrCP1 0.049 0.075 0.25 7 -10000 0 7
FZD1 0.015 0.001 -10000 0 -10000 0 0
AXIN2 -0.086 0.36 -10000 0 -1.4 18 18
AXIN1 0.016 0.001 -10000 0 -10000 0 0
RAN 0.015 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.019 0.036 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.081 0.059 0.25 1 -0.3 1 2
Axin1/APC/GSK3 0.016 0.044 0.23 4 -10000 0 4
Axin1/APC/GSK3/beta catenin/Macf1 0.063 0.032 -10000 0 -10000 0 0
HNF1A 0.011 0.067 -10000 0 -0.49 4 4
CTBP1 0.017 0.04 -10000 0 -0.46 1 1
MYC -0.069 0.33 -10000 0 -1.5 13 13
RANBP3 0.015 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.16 0.19 -10000 0 -0.33 140 140
NKD1 -0.017 0.13 -10000 0 -0.54 15 15
TCF4 0.012 0.066 -10000 0 -0.55 3 3
TCF3 0.019 0.026 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.031 0.022 -10000 0 -10000 0 0
Ran/GTP 0.012 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.054 0.16 0.48 30 -10000 0 30
LEF1 0.01 0.073 -10000 0 -0.48 5 5
DVL1 0.06 0.04 -10000 0 -10000 0 0
CSNK2A1 0.015 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.066 0.083 -10000 0 -0.34 1 1
DKK1/LRP6/Kremen 2 -0.14 0.19 -10000 0 -0.32 128 128
LRP6 0.015 0.001 -10000 0 -10000 0 0
CSNK1A1 0.017 0.031 -10000 0 -10000 0 0
NLK 0.014 0.005 -10000 0 -10000 0 0
CCND1 -0.033 0.21 -10000 0 -1.2 6 6
WNT1 0.01 0.031 -10000 0 -0.48 1 1
GSK3A 0.016 0.001 -10000 0 -10000 0 0
GSK3B 0.015 0.001 -10000 0 -10000 0 0
FRAT1 0.015 0 -10000 0 -10000 0 0
PPP2R5D 0.046 0.067 0.3 15 -10000 0 15
APC 0.042 0.016 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.074 0.092 0.24 58 -10000 0 58
CREBBP 0.019 0.026 -10000 0 -10000 0 0
Visual signal transduction: Rods

Figure S64.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S64.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:K + 0.015 0 -9999 0 -10000 0 0
GNAT1/GTP 0.006 0.022 -9999 0 -0.35 1 1
Metarhodopsin II/Arrestin 0.002 0.004 -9999 0 -10000 0 0
PDE6G/GNAT1/GTP 0.006 0.058 -9999 0 -0.29 10 10
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.008 0.031 -9999 0 -0.48 1 1
GRK1 0.001 0.004 -9999 0 -10000 0 0
CNG Channel -0.13 0.15 -9999 0 -0.45 31 31
mol:Na + -0.15 0.15 -9999 0 -0.45 31 31
mol:ADP 0.001 0.004 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.065 0.17 -9999 0 -0.35 67 67
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.15 0.15 -9999 0 -0.46 31 31
CNGB1 -0.2 0.25 -9999 0 -0.48 115 115
RDH5 0.013 0.036 -9999 0 -0.57 1 1
SAG 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.12 0.16 -9999 0 -0.43 31 31
Na + (4 Units) -0.14 0.14 -9999 0 -0.42 31 31
RGS9 -0.11 0.24 -9999 0 -0.57 57 57
GNB1/GNGT1 0.002 0.08 -9999 0 -0.34 14 14
GNAT1/GDP -0.051 0.14 -9999 0 -0.3 65 65
GUCY2D -0.042 0.15 -9999 0 -0.48 29 29
GNGT1 -0.013 0.11 -9999 0 -0.48 14 14
GUCY2F 0.002 0.005 -9999 0 -10000 0 0
GNB5 0.015 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.008 0.08 -9999 0 -0.29 9 9
mol:11-cis-retinal 0.013 0.035 -9999 0 -0.56 1 1
mol:cGMP -0.015 0.097 -9999 0 -0.38 2 2
GNB1 0.015 0 -9999 0 -10000 0 0
Rhodopsin 0.012 0.027 -9999 0 -0.42 1 1
SLC24A1 0.015 0 -9999 0 -10000 0 0
CNGA1 -0.051 0.18 -9999 0 -0.52 33 33
Metarhodopsin II 0.003 0.005 -9999 0 -10000 0 0
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.018 0.1 -9999 0 -0.41 2 2
RGS9BP -0.013 0.12 -9999 0 -0.55 13 13
Metarhodopsin II/Transducin 0.012 0.032 -9999 0 -10000 0 0
GCAP Family/Ca ++ 0.004 0.06 -9999 0 -0.26 13 13
PDE6A/B 0.002 0.088 -9999 0 -0.39 13 13
mol:Pi -0.065 0.17 -9999 0 -0.35 67 67
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin 0.009 0.063 -9999 0 -0.25 15 15
PDE6B -0.005 0.1 -9999 0 -0.57 9 9
PDE6A 0.006 0.061 -9999 0 -0.48 4 4
PDE6G -0.002 0.09 -9999 0 -0.48 9 9
RHO 0.004 0.006 -9999 0 -10000 0 0
PDE6 -0.085 0.14 -9999 0 -0.57 7 7
GUCA1A -0.009 0.099 -9999 0 -0.48 11 11
GC2/GCAP Family 0.005 0.061 -9999 0 -0.32 1 1
GUCA1C -0.001 0.03 -9999 0 -0.48 1 1
GUCA1B 0.013 0.036 -9999 0 -0.57 1 1
Sphingosine 1-phosphate (S1P) pathway

Figure S65.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S65.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.013 0.03 -9999 0 -0.48 1 1
SPHK1 -0.049 0.17 -9999 0 -0.49 34 34
GNAI2 0.015 0 -9999 0 -10000 0 0
mol:S1P 0.005 0.054 -9999 0 -0.29 1 1
GNAO1 -0.16 0.27 -9999 0 -0.57 80 80
mol:Sphinganine-1-P -0.022 0.12 -9999 0 -0.34 35 35
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.03 0.039 -9999 0 -10000 0 0
GNAI3 0.015 0 -9999 0 -10000 0 0
G12/G13 0.022 0 -9999 0 -10000 0 0
S1PR3 0 0.091 -9999 0 -0.55 7 7
S1PR2 0.015 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.015 0.038 -9999 0 -0.25 1 1
S1PR5 -0.008 0.11 -9999 0 -0.5 12 12
S1PR4 0.003 0.08 -9999 0 -0.52 6 6
GNAI1 0.013 0.036 -9999 0 -0.57 1 1
S1P/S1P5/G12 0.008 0.071 -9999 0 -0.26 12 12
S1P/S1P3/Gq -0.02 0.12 -9999 0 -0.26 44 44
S1P/S1P4/Gi -0.1 0.19 -9999 0 -0.44 46 46
GNAQ 0.015 0 -9999 0 -10000 0 0
GNAZ -0.12 0.24 -9999 0 -0.57 60 60
GNA14 -0.079 0.21 -9999 0 -0.57 43 43
GNA15 0.011 0.05 -9999 0 -0.57 2 2
GNA12 0.015 0 -9999 0 -10000 0 0
GNA13 0.015 0 -9999 0 -10000 0 0
GNA11 0.013 0.036 -9999 0 -0.57 1 1
ABCC1 0.011 0.043 -9999 0 -0.48 2 2
ErbB4 signaling events

Figure S66.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S66.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.023 0.066 -9999 0 -0.32 8 8
epithelial cell differentiation -0.04 0.087 -9999 0 -0.42 4 4
ITCH 0.016 0.032 -9999 0 -0.48 1 1
WWP1 0.033 0.029 -9999 0 -10000 0 0
FYN 0.009 0.061 -9999 0 -0.57 3 3
EGFR -0.007 0.11 -9999 0 -0.52 11 11
PRL -0.002 0.06 -9999 0 -0.48 4 4
neuron projection morphogenesis 0.007 0.12 -9999 0 -10000 0 0
PTPRZ1 -0.16 0.26 -9999 0 -0.54 84 84
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.011 0.12 -9999 0 -0.34 1 1
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.039 0.14 -9999 0 -0.3 50 50
ADAM17 0.018 0.008 -9999 0 -10000 0 0
ErbB4/ErbB4 0.032 0.037 -9999 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.005 0.056 -9999 0 -0.31 1 1
NCOR1 0.015 0 -9999 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.032 0.14 -9999 0 -0.34 13 13
GRIN2B -0.034 0.14 -9999 0 -0.47 6 6
ErbB4/ErbB2/betacellulin -0.005 0.12 -9999 0 -0.4 4 4
STAT1 0.009 0.053 -9999 0 -0.48 3 3
HBEGF -0.002 0.099 -9999 0 -0.57 8 8
PRLR -0.043 0.16 -9999 0 -0.52 29 29
E4ICDs/ETO2 0.021 0.068 -9999 0 -0.31 9 9
axon guidance 0.029 0.1 -9999 0 -0.29 5 5
NEDD4 0.018 0.008 -9999 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin -0.032 0.13 -9999 0 -0.36 33 33
CBFA2T3 -0.004 0.1 -9999 0 -0.57 9 9
ErbB4/ErbB2/HBEGF 0.025 0.078 -9999 0 -0.38 3 3
MAPK3 -0.002 0.12 -9999 0 -10000 0 0
STAT1 (dimer) 0.03 0.042 -9999 0 -10000 0 0
MAPK1 -0.002 0.12 -9999 0 -10000 0 0
JAK2 0.013 0.036 -9999 0 -0.57 1 1
ErbB4/ErbB2/neuregulin 1 beta -0.037 0.14 -9999 0 -0.32 12 12
NRG1 -0.073 0.18 -9999 0 -0.39 63 63
NRG3 -0.007 0.084 -9999 0 -0.48 8 8
NRG2 -0.23 0.29 -9999 0 -0.57 113 113
NRG4 -0.038 0.17 -9999 0 -0.57 24 24
heart development 0.029 0.1 -9999 0 -0.29 5 5
neural crest cell migration -0.037 0.14 -9999 0 -0.32 12 12
ERBB2 0.015 0.066 -9999 0 -0.34 9 9
WWOX/E4ICDs 0.032 0.036 -9999 0 -0.31 1 1
SHC1 0.013 0.03 -9999 0 -0.48 1 1
ErbB4/EGFR/neuregulin 4 -0.002 0.12 -9999 0 -0.48 5 5
apoptosis 0.014 0.044 -9999 0 -10000 0 0
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.12 0.17 -9999 0 -0.32 113 113
ErbB4/ErbB2/epiregulin -0.046 0.14 -9999 0 -0.39 10 10
ErbB4/ErbB4/betacellulin/betacellulin -0.01 0.12 -9999 0 -0.32 32 32
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.033 0.089 -9999 0 -0.42 2 2
MDM2 0.028 0.059 -9999 0 -0.31 1 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.059 0.12 -9999 0 -0.32 11 11
STAT5A 0.036 0.1 -9999 0 -0.39 1 1
ErbB4/EGFR/neuregulin 1 beta -0.04 0.15 -9999 0 -0.38 14 14
DLG4 0.015 0 -9999 0 -10000 0 0
GRB2/SHC 0.021 0.022 -9999 0 -0.34 1 1
E4ICDs/TAB2/NCoR1 -0.004 0.017 -9999 0 -10000 0 0
STAT5A (dimer) -0.041 0.093 -9999 0 -0.46 4 4
MAP3K7IP2 0 0 -9999 0 -10000 0 0
STAT5B (dimer) 0.034 0.094 -9999 0 -10000 0 0
LRIG1 -0.028 0.15 -9999 0 -0.57 20 20
EREG -0.13 0.24 -9999 0 -0.52 73 73
BTC -0.055 0.19 -9999 0 -0.57 32 32
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.029 0.1 -9999 0 -0.3 5 5
ERBB4 0.032 0.037 -9999 0 -10000 0 0
STAT5B 0.015 0 -9999 0 -10000 0 0
YAP1 -0.001 0.013 -9999 0 -10000 0 0
GRB2 0.015 0 -9999 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.005 0.11 -9999 0 -0.44 5 5
glial cell differentiation 0.004 0.017 -9999 0 -10000 0 0
WWOX 0.013 0.036 -9999 0 -0.57 1 1
cell proliferation -0.054 0.16 -9999 0 -0.43 12 12
Effects of Botulinum toxin

Figure S67.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S67.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
STX1A 0.007 0.044 -9999 0 -0.35 4 4
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.001 0.087 -9999 0 -0.4 12 12
STXBP1 -0.007 0.11 -9999 0 -0.57 10 10
ACh/CHRNA1 -0.049 0.12 -9999 0 -0.31 47 47
RAB3GAP2/RIMS1/UNC13B 0.011 0.074 -9999 0 -0.33 12 12
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 -0.016 0.12 -9999 0 -0.56 12 12
mol:ACh -0.003 0.039 -9999 0 -0.12 23 23
RAB3GAP2 0.015 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.034 0.088 -9999 0 -0.36 10 10
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.049 0.12 -9999 0 -0.31 47 47
UNC13B 0.015 0 -9999 0 -10000 0 0
CHRNA1 -0.074 0.19 -9999 0 -0.48 47 47
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.031 0.12 -9999 0 -0.38 28 28
SNAP25 -0.021 0.086 -9999 0 -0.25 30 30
VAMP2 0.008 0 -9999 0 -10000 0 0
SYT1 -0.044 0.17 -9999 0 -0.55 28 28
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 0.002 0.078 -9999 0 -0.33 14 14
STX1A/SNAP25 fragment 1/VAMP2 -0.034 0.088 -9999 0 -0.36 10 10
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

Figure S68.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S68.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HIF3A -0.28 0.29 -9999 0 -0.57 134 134
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.013 0.03 -9999 0 -0.48 1 1
TCEB1 0.015 0 -9999 0 -10000 0 0
HIF1A/p53 0.034 0.016 -9999 0 -10000 0 0
HIF1A 0.026 0.017 -9999 0 -10000 0 0
COPS5 0.015 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.044 0.016 -9999 0 -10000 0 0
FIH (dimer) 0.015 0 -9999 0 -10000 0 0
CDKN2A -0.22 0.25 -9999 0 -0.49 127 127
ARNT/IPAS -0.19 0.21 -9999 0 -0.41 134 134
HIF1AN 0.015 0 -9999 0 -10000 0 0
GNB2L1 0.015 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.034 0.016 -9999 0 -10000 0 0
CUL2 0.015 0 -9999 0 -10000 0 0
OS9 0.015 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.03 0.019 -9999 0 -0.27 1 1
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.034 0.016 -9999 0 -10000 0 0
PHD1-3/OS9 0.031 0.05 -9999 0 -0.3 6 6
HIF1A/RACK1/Elongin B/Elongin C -0.002 0.013 -9999 0 -10000 0 0
VHL 0.015 0 -9999 0 -10000 0 0
HSP90AA1 0.015 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.034 0.016 -9999 0 -10000 0 0
EGLN3 0.002 0.086 -9999 0 -0.57 6 6
EGLN2 0.015 0 -9999 0 -10000 0 0
EGLN1 0.015 0 -9999 0 -10000 0 0
TP53 0.015 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.043 0.009 -9999 0 -10000 0 0
ARNT 0.015 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.015 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.08 0.12 -9999 0 -0.27 7 7
ErbB2/ErbB3 signaling events

Figure S69.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S69.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.02 0.005 -9999 0 -10000 0 0
RAS family/GTP -0.021 0.12 -9999 0 -0.5 4 4
NFATC4 -0.024 0.11 -9999 0 -0.38 5 5
ERBB2IP 0.016 0.003 -9999 0 -10000 0 0
HSP90 (dimer) 0.015 0 -9999 0 -10000 0 0
mammary gland morphogenesis -0.044 0.12 -9999 0 -0.45 4 4
JUN 0.003 0.082 -9999 0 -0.34 1 1
HRAS 0.015 0.001 -9999 0 -10000 0 0
DOCK7 -0.036 0.12 -9999 0 -0.43 4 4
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.065 0.14 -9999 0 -0.31 52 52
AKT1 0.012 0.003 -9999 0 -10000 0 0
BAD 0.021 0.003 -9999 0 -10000 0 0
MAPK10 -0.017 0.095 -9999 0 -0.28 11 11
mol:GTP -0.001 0.002 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.046 0.14 -9999 0 -0.49 4 4
RAF1 -0.013 0.12 -9999 0 -0.54 3 3
ErbB2/ErbB3/neuregulin 2 -0.14 0.18 -9999 0 -0.33 117 117
STAT3 0.003 0.005 -9999 0 -10000 0 0
cell migration -0.005 0.088 -9999 0 -0.24 11 11
mol:PI-3-4-5-P3 -0.001 0.002 -9999 0 -10000 0 0
cell proliferation -0.082 0.23 -9999 0 -0.51 35 35
FOS -0.12 0.27 -9999 0 -0.5 81 81
NRAS 0.015 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.044 0.12 -9999 0 -0.45 4 4
MAPK3 -0.051 0.18 -9999 0 -0.54 12 12
MAPK1 -0.051 0.18 -9999 0 -0.54 12 12
JAK2 -0.037 0.12 -9999 0 -0.43 4 4
NF2 -0.001 0.004 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.039 0.13 -9999 0 -0.28 52 52
NRG1 -0.12 0.24 -9999 0 -0.55 63 63
GRB2/SOS1 0.022 0.001 -9999 0 -10000 0 0
MAPK8 -0.033 0.12 -9999 0 -0.28 21 21
MAPK9 0.002 0.072 -9999 0 -0.21 3 3
ERBB2 -0.012 0.064 -9999 0 -0.35 9 9
ERBB3 0.001 0.085 -9999 0 -0.56 6 6
SHC1 0.013 0.03 -9999 0 -0.48 1 1
RAC1 0.015 0 -9999 0 -10000 0 0
apoptosis 0.005 0.012 -9999 0 -10000 0 0
STAT3 (dimer) 0.021 0.006 -9999 0 -10000 0 0
RNF41 0.026 0.008 -9999 0 -10000 0 0
FRAP1 0.01 0.003 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.043 0.074 -9999 0 -0.3 4 4
ErbB2/ErbB2/HSP90 (dimer) -0.01 0.052 -9999 0 -0.29 9 9
CHRNA1 -0.048 0.17 -9999 0 -0.4 25 25
myelination -0.016 0.11 -9999 0 -0.35 5 5
PPP3CB -0.033 0.11 -9999 0 -0.4 4 4
KRAS 0.013 0.03 -9999 0 -0.48 1 1
RAC1-CDC42/GDP -0.017 0.11 -9999 0 -0.44 4 4
NRG2 -0.23 0.29 -9999 0 -0.57 113 113
mol:GDP -0.039 0.13 -9999 0 -0.28 52 52
SOS1 0.015 0.001 -9999 0 -10000 0 0
MAP2K2 -0.008 0.12 -9999 0 -0.45 5 5
SRC 0.015 0 -9999 0 -10000 0 0
mol:cAMP -0.001 0.002 -9999 0 -10000 0 0
PTPN11 -0.033 0.12 -9999 0 -0.43 4 4
MAP2K1 -0.065 0.18 -9999 0 -0.48 20 20
heart morphogenesis -0.044 0.12 -9999 0 -0.45 4 4
RAS family/GDP -0.021 0.11 -9999 0 -0.49 4 4
GRB2 0.015 0.001 -9999 0 -10000 0 0
PRKACA -0.004 0.007 -9999 0 -10000 0 0
CHRNE 0.013 0.025 -9999 0 -0.18 2 2
HSP90AA1 0.015 0 -9999 0 -10000 0 0
activation of caspase activity -0.012 0.003 -9999 0 -10000 0 0
nervous system development -0.044 0.12 -9999 0 -0.45 4 4
CDC42 0.015 0 -9999 0 -10000 0 0
Caspase cascade in apoptosis

Figure S70.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S70.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TOP1 -0.001 0.12 -10000 0 -0.34 23 23
ACTA1 -0.02 0.15 -10000 0 -0.43 25 25
NUMA1 -0.001 0.12 -10000 0 -0.34 23 23
SPTAN1 -0.015 0.15 -10000 0 -0.43 23 23
LIMK1 -0.015 0.15 -10000 0 -0.43 23 23
BIRC3 -0.019 0.14 -10000 0 -0.56 16 16
BIRC2 0.011 0.043 -10000 0 -0.48 2 2
BAX 0.015 0 -10000 0 -10000 0 0
CASP10 -0.031 0.16 -10000 0 -0.4 40 40
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.013 0.03 -10000 0 -0.48 1 1
PTK2 -0.001 0.12 -10000 0 -0.34 23 23
DIABLO 0.015 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.015 0.15 -10000 0 -0.43 23 23
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.015 0 -10000 0 -10000 0 0
GSN -0.021 0.16 -10000 0 -0.42 28 28
MADD 0.015 0 -10000 0 -10000 0 0
TFAP2A 0.021 0.027 -10000 0 -10000 0 0
BID -0.005 0.083 -10000 0 -0.23 26 26
MAP3K1 0.003 0.054 -10000 0 -0.2 5 5
TRADD 0.015 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.023 0.002 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.015 0.15 -10000 0 -0.43 23 23
CASP9 0.015 0 -10000 0 -10000 0 0
DNA repair -0.006 0.05 -10000 0 -0.19 9 9
neuron apoptosis 0.019 0.07 -10000 0 -0.77 2 2
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.006 0.14 -10000 0 -0.41 23 23
APAF1 0.015 0 -10000 0 -10000 0 0
CASP6 0.02 0.072 -10000 0 -0.35 2 2
TRAF2 0.015 0 -10000 0 -10000 0 0
ICAD/CAD -0.007 0.14 -10000 0 -0.41 23 23
CASP7 0.008 0.071 0.29 14 -10000 0 14
KRT18 0.013 0.046 -10000 0 -0.63 1 1
apoptosis 0 0.14 -10000 0 -0.38 23 23
DFFA -0.015 0.15 -10000 0 -0.43 23 23
DFFB -0.015 0.15 -10000 0 -0.43 23 23
PARP1 0.006 0.05 0.19 9 -10000 0 9
actin filament polymerization 0.007 0.14 0.4 23 -10000 0 23
TNF -0.009 0.11 -10000 0 -0.48 13 13
CYCS 0 0.063 -10000 0 -0.2 13 13
SATB1 0.014 0.092 -10000 0 -0.35 4 4
SLK -0.015 0.15 -10000 0 -0.43 23 23
p15 BID/BAX 0.003 0.074 -10000 0 -0.3 5 5
CASP2 0.041 0.049 -10000 0 -10000 0 0
JNK cascade -0.003 0.054 0.2 5 -10000 0 5
CASP3 -0.025 0.16 -10000 0 -0.46 23 23
LMNB2 0.04 0.042 -10000 0 -10000 0 0
RIPK1 0.015 0 -10000 0 -10000 0 0
CASP4 0.013 0.03 -10000 0 -0.48 1 1
Mammalian IAPs/DIABLO 0.016 0.086 -10000 0 -0.31 15 15
negative regulation of DNA binding 0.021 0.027 -10000 0 -10000 0 0
stress fiber formation -0.015 0.15 -10000 0 -0.43 23 23
GZMB -0.049 0.19 -10000 0 -0.47 40 40
CASP1 0.008 0.063 -10000 0 -0.34 8 8
LMNB1 0.04 0.042 -10000 0 -10000 0 0
APP 0.019 0.071 -10000 0 -0.78 2 2
TNFRSF1A 0.015 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.013 0 -10000 0 -10000 0 0
VIM -0.005 0.13 0.22 9 -0.38 23 32
LMNA 0.04 0.042 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.035 0.052 -10000 0 -10000 0 0
LRDD 0.015 0 -10000 0 -10000 0 0
SREBF1 -0.016 0.15 -10000 0 -0.43 23 23
APAF-1/Caspase 9 0.002 0.044 0.33 1 -10000 0 1
nuclear fragmentation during apoptosis -0.001 0.12 -10000 0 -0.33 23 23
CFL2 -0.008 0.14 -10000 0 -0.4 23 23
GAS2 -0.048 0.18 -10000 0 -0.38 45 45
positive regulation of apoptosis 0.044 0.041 -10000 0 -10000 0 0
PRF1 -0.023 0.14 -10000 0 -0.53 19 19
Regulation of Androgen receptor activity

Figure S71.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S71.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.025 0.003 -9999 0 -10000 0 0
SMARCC1 0.011 0.013 -9999 0 -10000 0 0
REL 0.012 0.046 -9999 0 -0.51 2 2
HDAC7 -0.018 0.14 -9999 0 -0.34 12 12
JUN -0.001 0.093 -9999 0 -0.57 7 7
EP300 0.015 0.001 -9999 0 -10000 0 0
KAT2B 0.015 0.001 -9999 0 -10000 0 0
KAT5 0.015 0.001 -9999 0 -10000 0 0
MAPK14 0.014 0.052 -9999 0 -0.39 4 4
FOXO1 0.015 0.001 -9999 0 -10000 0 0
T-DHT/AR -0.025 0.14 -9999 0 -0.36 19 19
MAP2K6 0.004 0.068 -9999 0 -0.54 4 4
BRM/BAF57 0.02 0.008 -9999 0 -10000 0 0
MAP2K4 0.012 0.008 -9999 0 -10000 0 0
SMARCA2 0.014 0.004 -9999 0 -10000 0 0
PDE9A -0.17 0.42 -9999 0 -1.2 35 35
NCOA2 -0.02 0.14 -9999 0 -0.57 16 16
CEBPA 0 0.087 -9999 0 -0.49 8 8
EHMT2 0.014 0.004 -9999 0 -10000 0 0
cell proliferation -0.009 0.15 -9999 0 -0.48 7 7
NR0B1 -0.03 0.13 -9999 0 -0.48 19 19
EGR1 -0.12 0.24 -9999 0 -0.57 62 62
RXRs/9cRA -0.076 0.15 -9999 0 -0.31 78 78
AR/RACK1/Src -0.019 0.091 -9999 0 -0.38 5 5
AR/GR -0.07 0.16 -9999 0 -0.32 49 49
GNB2L1 0.015 0.001 -9999 0 -10000 0 0
PKN1 0.013 0.036 -9999 0 -0.57 1 1
RCHY1 0.015 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity -0.001 0.002 -9999 0 -10000 0 0
MAPK8 0.015 0.048 -9999 0 -0.41 3 3
T-DHT/AR/TIF2/CARM1 -0.022 0.12 -9999 0 -0.46 7 7
SRC 0.023 0.059 -9999 0 -0.3 1 1
NR3C1 0 0.093 -9999 0 -0.57 7 7
KLK3 -0.14 0.29 -9999 0 -1 20 20
APPBP2 0.012 0.008 -9999 0 -10000 0 0
TRIM24 0.01 0.044 -9999 0 -0.49 2 2
T-DHT/AR/TIP60 -0.011 0.094 -9999 0 -0.4 5 5
TMPRSS2 -0.22 0.46 -9999 0 -1.2 48 48
RXRG -0.16 0.26 -9999 0 -0.57 78 78
mol:9cRA 0 0.002 -9999 0 -10000 0 0
RXRA 0.013 0.035 -9999 0 -0.57 1 1
RXRB 0.015 0.001 -9999 0 -10000 0 0
CARM1 0.015 0.002 -9999 0 -10000 0 0
NR2C2 0.011 0.047 -9999 0 -0.52 2 2
KLK2 -0.034 0.15 -9999 0 -0.41 19 19
AR -0.076 0.16 -9999 0 -0.29 90 90
SENP1 0.015 0.001 -9999 0 -10000 0 0
HSP90AA1 0.015 0 -9999 0 -10000 0 0
MDM2 0.002 0.086 -9999 0 -0.48 8 8
SRY 0.001 0.061 -9999 0 -0.48 4 4
GATA2 -0.009 0.11 -9999 0 -0.52 12 12
MYST2 0.015 0.001 -9999 0 -10000 0 0
HOXB13 -0.075 0.2 -9999 0 -0.56 41 41
T-DHT/AR/RACK1/Src -0.006 0.094 -9999 0 -0.38 5 5
positive regulation of transcription -0.009 0.11 -9999 0 -0.52 12 12
DNAJA1 0.012 0.008 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.03 0.021 -9999 0 -10000 0 0
NCOA1 0.019 0.006 -9999 0 -10000 0 0
SPDEF -0.091 0.22 -9999 0 -0.53 51 51
T-DHT/AR/TIF2 0.001 0.092 -9999 0 -0.36 6 6
T-DHT/AR/Hsp90 -0.012 0.094 -9999 0 -0.4 5 5
GSK3B 0.014 0.005 -9999 0 -10000 0 0
NR2C1 0.016 0.002 -9999 0 -10000 0 0
mol:T-DHT 0.016 0.063 -9999 0 -0.3 6 6
SIRT1 0.015 0.001 -9999 0 -10000 0 0
ZMIZ2 0.017 0.008 -9999 0 -10000 0 0
POU2F1 0.015 0.045 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 -0.049 0.1 -9999 0 -0.38 9 9
CREBBP 0.015 0.001 -9999 0 -10000 0 0
SMARCE1 0.014 0.004 -9999 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

Figure S72.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S72.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MET/RANBP9 0.022 0 -9999 0 -10000 0 0
CRKL -0.012 0.1 -9999 0 -0.35 3 3
mol:PIP3 -0.021 0.006 -9999 0 -10000 0 0
AKT1 0.003 0.005 -9999 0 -10000 0 0
PTK2B 0.013 0.036 -9999 0 -0.57 1 1
RAPGEF1 -0.004 0.099 -9999 0 -0.36 2 2
RANBP10 0.015 0 -9999 0 -10000 0 0
PIK3CA 0.015 0 -9999 0 -10000 0 0
HGF/MET/SHIP2 -0.059 0.16 -9999 0 -0.33 66 66
MAP3K5 0.003 0.1 -9999 0 -0.34 3 3
HGF/MET/CIN85/CBL/ENDOPHILINS -0.043 0.14 -9999 0 -0.3 60 60
AP1 -0.1 0.19 -9999 0 -0.38 81 81
mol:SU11274 0 0 -9999 0 -10000 0 0
SHC1 0.013 0.03 -9999 0 -0.48 1 1
apoptosis -0.21 0.35 -9999 0 -0.74 81 81
STAT3 (dimer) -0.017 0.12 -9999 0 -0.48 1 1
GAB1/CRKL/SHP2/PI3K -0.037 0.069 -9999 0 -0.37 1 1
INPP5D 0.002 0.086 -9999 0 -0.57 6 6
CBL/CRK -0.001 0.097 -9999 0 -0.33 1 1
PTPN11 0.015 0 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
PLCG1 0.015 0 -9999 0 -10000 0 0
PTEN 0.015 0 -9999 0 -10000 0 0
ELK1 -0.003 0.009 -9999 0 -10000 0 0
mol:SU5416 0 0 -9999 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.033 0.061 -9999 0 -0.39 1 1
PAK1 0.009 0.019 -9999 0 -0.29 1 1
HGF/MET/RANBP10 -0.059 0.16 -9999 0 -0.34 60 60
HRAS -0.032 0.14 -9999 0 -0.38 1 1
DOCK1 -0.005 0.1 -9999 0 -0.36 2 2
GAB1 -0.02 0.1 -9999 0 -0.34 2 2
CRK -0.011 0.1 -9999 0 -0.31 2 2
mol:PHA665752 0 0 -9999 0 -10000 0 0
mol:GDP -0.11 0.2 -9999 0 -0.47 60 60
JUN 0 0.093 -9999 0 -0.57 7 7
EntrezGene:200958 0 0 -9999 0 -10000 0 0
HGF/MET -0.034 0.094 -9999 0 -0.2 60 60
PIK3R1 0.015 0 -9999 0 -10000 0 0
cell morphogenesis 0.009 0.13 -9999 0 -0.41 2 2
GRB2/SHC -0.013 0.085 -9999 0 -0.41 1 1
FOS -0.16 0.27 -9999 0 -0.57 80 80
GLMN 0 0 -9999 0 -10000 0 0
cell motility -0.003 0.009 -9999 0 -10000 0 0
HGF/MET/MUC20 -0.069 0.16 -9999 0 -0.34 66 66
cell migration -0.013 0.084 -9999 0 -0.4 1 1
GRB2 0.015 0 -9999 0 -10000 0 0
CBL 0.015 0 -9999 0 -10000 0 0
MET/RANBP10 0.022 0 -9999 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.025 0.12 -9999 0 -0.5 1 1
MET/MUC20 0.011 0 -9999 0 -10000 0 0
RAP1B 0.005 0.095 -9999 0 -0.34 2 2
RAP1A 0.005 0.095 -9999 0 -0.34 2 2
HGF/MET/RANBP9 -0.059 0.16 -9999 0 -0.33 66 66
RAF1 -0.023 0.13 -9999 0 -0.35 1 1
STAT3 -0.018 0.12 -9999 0 -0.49 1 1
cell proliferation -0.028 0.16 -9999 0 -0.5 2 2
RPS6KB1 -0.004 0.036 -9999 0 -10000 0 0
MAPK3 -0.008 0.007 -9999 0 -10000 0 0
MAPK1 -0.008 0.007 -9999 0 -10000 0 0
RANBP9 0.015 0 -9999 0 -10000 0 0
MAPK8 0.019 0.098 -9999 0 -0.4 3 3
SRC -0.014 0.11 -9999 0 -0.46 1 1
PI3K -0.012 0.084 -9999 0 -0.41 1 1
MET/Glomulin 0.014 0 -9999 0 -10000 0 0
SOS1 0.015 0 -9999 0 -10000 0 0
MAP2K1 -0.013 0.12 -9999 0 -10000 0 0
MET 0.015 0 -9999 0 -10000 0 0
MAP4K1 -0.006 0.1 -9999 0 -0.37 3 3
PTK2 0.015 0 -9999 0 -10000 0 0
MAP2K2 -0.013 0.12 -9999 0 -10000 0 0
BAD 0.01 0.005 -9999 0 -10000 0 0
MAP2K4 0.011 0.094 -9999 0 -0.32 2 2
SHP2/GRB2/SOS1/GAB1 -0.037 0.068 -9999 0 -10000 0 0
INPPL1 0.015 0 -9999 0 -10000 0 0
PXN 0.015 0 -9999 0 -10000 0 0
SH3KBP1 0.015 0 -9999 0 -10000 0 0
HGS -0.023 0.087 -9999 0 -0.44 1 1
PLCgamma1/PKC 0.011 0 -9999 0 -10000 0 0
HGF -0.13 0.25 -9999 0 -0.56 66 66
RASA1 0.015 0 -9999 0 -10000 0 0
NCK1 0.015 0 -9999 0 -10000 0 0
PTPRJ 0.013 0.036 -9999 0 -0.57 1 1
NCK/PLCgamma1 -0.016 0.094 -9999 0 -0.43 1 1
PDPK1 -0.008 0.005 -9999 0 -10000 0 0
HGF/MET/SHIP -0.067 0.17 -9999 0 -0.34 69 69
IL27-mediated signaling events

Figure S73.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S73.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.019 0.005 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.025 0.12 0.46 5 -10000 0 5
IL27/IL27R/JAK1 -0.052 0.15 -10000 0 -0.62 4 4
TBX21 -0.037 0.18 -10000 0 -0.48 18 18
IL12B -0.004 0.08 -10000 0 -0.49 7 7
IL12A 0.006 0.044 -10000 0 -0.35 4 4
IL6ST -0.077 0.21 -10000 0 -0.57 41 41
IL27RA/JAK1 0.016 0.031 -10000 0 -10000 0 0
IL27 -0.016 0.11 -10000 0 -0.49 14 14
TYK2 0.014 0.007 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.12 0.15 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.025 0.12 0.46 5 -10000 0 5
T cell proliferation during immune response 0.025 0.12 0.46 5 -10000 0 5
MAPKKK cascade -0.025 0.12 -10000 0 -0.46 5 5
STAT3 0.015 0 -10000 0 -10000 0 0
STAT2 0.015 0 -10000 0 -10000 0 0
STAT1 0.009 0.052 -10000 0 -0.48 3 3
IL12RB1 -0.021 0.13 -10000 0 -0.51 18 18
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.066 0.21 -10000 0 -0.49 30 30
IL27/IL27R/JAK2/TYK2 -0.025 0.12 -10000 0 -0.47 5 5
positive regulation of T cell mediated cytotoxicity -0.025 0.12 -10000 0 -0.46 5 5
STAT1 (dimer) -0.072 0.2 0.5 10 -0.57 12 22
JAK2 0.011 0.036 -10000 0 -0.57 1 1
JAK1 0.015 0.003 -10000 0 -10000 0 0
STAT2 (dimer) -0.017 0.12 -10000 0 -0.44 5 5
T cell proliferation -0.15 0.19 -10000 0 -0.47 35 35
IL12/IL12R/TYK2/JAK2 0.005 0.076 -10000 0 -10000 0 0
IL17A -0.12 0.15 -10000 0 -10000 0 0
mast cell activation 0.025 0.12 0.46 5 -10000 0 5
IFNG -0.006 0.032 -10000 0 -0.088 5 5
T cell differentiation -0.005 0.006 -10000 0 -0.018 25 25
STAT3 (dimer) -0.017 0.12 -10000 0 -0.44 5 5
STAT5A (dimer) -0.018 0.12 -10000 0 -0.44 5 5
STAT4 (dimer) -0.031 0.13 -10000 0 -0.46 8 8
STAT4 -0.013 0.12 -10000 0 -0.57 13 13
T cell activation -0.01 0.007 0.047 2 -10000 0 2
IL27R/JAK2/TYK2 -0.027 0.12 -10000 0 -0.58 1 1
GATA3 -0.078 0.36 -10000 0 -1.4 19 19
IL18 0.005 0.058 -10000 0 -0.42 5 5
positive regulation of mast cell cytokine production -0.017 0.12 -10000 0 -0.43 5 5
IL27/EBI3 -0.011 0.1 -10000 0 -0.38 19 19
IL27RA 0.006 0.032 -10000 0 -10000 0 0
IL6 -0.24 0.29 -10000 0 -0.56 121 121
STAT5A 0.013 0.036 -10000 0 -0.57 1 1
monocyte differentiation 0 0.002 -10000 0 -10000 0 0
IL2 0.003 0.017 -10000 0 -10000 0 0
IL1B -0.026 0.12 -10000 0 -0.38 26 26
EBI3 -0.001 0.082 -10000 0 -0.5 7 7
TNF -0.005 0.077 -10000 0 -0.35 13 13
IL2 signaling events mediated by STAT5

Figure S74.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S74.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GAB2 0.016 0 -9999 0 -10000 0 0
ELF1 -0.007 0.094 -9999 0 -0.34 15 15
CCNA2 -0.12 0.22 -9999 0 -0.48 72 72
PIK3CA 0.016 0 -9999 0 -10000 0 0
JAK3 0.012 0.043 -9999 0 -0.48 2 2
PIK3R1 0.016 0 -9999 0 -10000 0 0
JAK1 0.016 0 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.055 0.11 -9999 0 -0.48 7 7
SHC1 0.014 0.03 -9999 0 -0.48 1 1
SP1 -0.004 0.098 -9999 0 -0.34 21 21
IL2RA -0.031 0.21 -9999 0 -0.58 29 29
IL2RB 0.005 0.079 -9999 0 -0.57 5 5
SOS1 0.016 0 -9999 0 -10000 0 0
IL2RG -0.011 0.12 -9999 0 -0.53 13 13
G1/S transition of mitotic cell cycle -0.064 0.26 -9999 0 -0.8 25 25
PTPN11 0.016 0 -9999 0 -10000 0 0
CCND2 -0.031 0.22 -9999 0 -0.8 21 21
LCK 0.005 0.077 -9999 0 -0.55 5 5
GRB2 0.016 0 -9999 0 -10000 0 0
IL2 0.006 0.007 -9999 0 -10000 0 0
CDK6 -0.007 0.11 -9999 0 -0.57 10 10
CCND3 0.062 0.098 -9999 0 -0.51 4 4
Hedgehog signaling events mediated by Gli proteins

Figure S75.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S75.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.015 0 -9999 0 -10000 0 0
HDAC2 0.015 0.001 -9999 0 -10000 0 0
GNB1/GNG2 0.009 0.079 -9999 0 -0.34 13 13
forebrain development -0.079 0.23 -9999 0 -0.57 37 37
GNAO1 -0.16 0.27 -9999 0 -0.57 80 80
SMO/beta Arrestin2 0.006 0.082 -9999 0 -0.41 10 10
SMO -0.007 0.11 -9999 0 -0.57 10 10
ARRB2 0.014 0.005 -9999 0 -10000 0 0
GLI3/SPOP 0.049 0.057 -9999 0 -10000 0 0
mol:GTP 0 0.002 -9999 0 -10000 0 0
GSK3B 0.015 0 -9999 0 -10000 0 0
GNAI2 0.015 0.002 -9999 0 -10000 0 0
SIN3/HDAC complex 0.039 0.002 -9999 0 -10000 0 0
GNAI1 0.013 0.036 -9999 0 -0.57 1 1
XPO1 0.015 0.007 -9999 0 -10000 0 0
GLI1/Su(fu) -0.083 0.18 -9999 0 -0.59 19 19
SAP30 0.015 0.001 -9999 0 -10000 0 0
mol:GDP -0.007 0.11 -9999 0 -0.56 10 10
MIM/GLI2A 0.016 0.008 -9999 0 -10000 0 0
IFT88 0.015 0 -9999 0 -10000 0 0
GNAI3 0.015 0.001 -9999 0 -10000 0 0
GLI2 0.023 0.072 -9999 0 -10000 0 0
GLI3 0.043 0.061 -9999 0 -0.24 8 8
CSNK1D 0.015 0 -9999 0 -10000 0 0
CSNK1E 0.015 0 -9999 0 -10000 0 0
SAP18 0.015 0 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.015 0 -9999 0 -10000 0 0
GNG2 0.009 0.061 -9999 0 -0.57 3 3
Gi family/GTP -0.11 0.21 -9999 0 -0.37 87 87
SIN3B 0.015 0.001 -9999 0 -10000 0 0
SIN3A 0.015 0 -9999 0 -10000 0 0
GLI3/Su(fu) 0.064 0.043 -9999 0 -10000 0 0
GLI2/Su(fu) 0.03 0.08 -9999 0 -10000 0 0
FOXA2 -0.053 0.11 -9999 0 -10000 0 0
neural tube patterning -0.079 0.23 -9999 0 -0.57 37 37
SPOP 0.015 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.03 0.04 -9999 0 -10000 0 0
GNB1 0.015 0 -9999 0 -10000 0 0
CSNK1G2 0.015 0 -9999 0 -10000 0 0
CSNK1G3 0.015 0 -9999 0 -10000 0 0
MTSS1 0.016 0.008 -9999 0 -10000 0 0
embryonic limb morphogenesis -0.079 0.23 -9999 0 -0.57 37 37
SUFU 0.021 0.045 -9999 0 -10000 0 0
LGALS3 0.013 0.036 -9999 0 -0.57 1 1
catabolic process 0.057 0.076 -9999 0 -10000 0 0
GLI3A/CBP -0.026 0.13 -9999 0 -0.34 37 37
KIF3A 0.015 0 -9999 0 -10000 0 0
GLI1 -0.082 0.24 -9999 0 -0.59 37 37
RAB23 0.013 0.036 -9999 0 -0.57 1 1
CSNK1A1 0.015 0 -9999 0 -10000 0 0
IFT172 0.015 0 -9999 0 -10000 0 0
RBBP7 0.015 0.001 -9999 0 -10000 0 0
Su(fu)/Galectin3 0.028 0.044 -9999 0 -0.29 1 1
GNAZ -0.12 0.24 -9999 0 -0.57 60 60
RBBP4 0.015 0 -9999 0 -10000 0 0
CSNK1G1 0.015 0 -9999 0 -10000 0 0
PIAS1 0.015 0 -9999 0 -10000 0 0
PRKACA 0.015 0 -9999 0 -10000 0 0
GLI2/SPOP 0.029 0.067 -9999 0 -10000 0 0
STK36 0.015 0.006 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.089 0.2 -9999 0 -0.46 43 43
PTCH1 -0.061 0.2 -9999 0 -0.77 10 10
MIM/GLI1 -0.083 0.24 -9999 0 -0.62 30 30
CREBBP -0.026 0.12 -9999 0 -0.34 37 37
Su(fu)/SIN3/HDAC complex 0.054 0.013 -9999 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

Figure S76.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S76.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ACADVL -0.002 0.23 -10000 0 -0.87 5 5
PCK1 -0.011 0.17 -10000 0 -0.56 8 8
HNF4A -0.029 0.27 -10000 0 -1.1 5 5
KCNJ11 -0.028 0.3 -10000 0 -0.88 18 18
AKT1 0.021 0.11 -10000 0 -10000 0 0
response to starvation -0.003 0.018 -10000 0 -10000 0 0
DLK1 -0.054 0.34 -10000 0 -0.98 22 22
NKX2-1 0.095 0.23 0.62 12 -10000 0 12
ACADM -0.005 0.23 -10000 0 -0.9 6 6
TAT -0.011 0.17 -10000 0 -0.69 6 6
CEBPB 0.011 0.037 -10000 0 -0.58 1 1
CEBPA -0.002 0.088 -10000 0 -0.5 8 8
TTR -0.082 0.22 -10000 0 -0.62 17 17
PKLR -0.02 0.24 -10000 0 -0.92 6 6
APOA1 -0.008 0.26 -10000 0 -1 5 5
CPT1C -0.006 0.23 -10000 0 -0.87 5 5
ALAS1 0.038 0.13 -10000 0 -10000 0 0
TFRC 0.003 0.18 -10000 0 -0.55 5 5
FOXF1 -0.18 0.28 -10000 0 -0.56 95 95
NF1 0.024 0 -10000 0 -10000 0 0
HNF1A (dimer) -0.02 0.074 -10000 0 -0.51 4 4
CPT1A -0.005 0.23 -10000 0 -0.89 6 6
HMGCS1 -0.002 0.23 -10000 0 -0.87 5 5
NR3C1 0.003 0.097 -10000 0 -0.57 7 7
CPT1B -0.004 0.23 -10000 0 -0.9 5 5
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 -0.012 0.039 -10000 0 -10000 0 0
GCK -0.048 0.32 -10000 0 -0.93 20 20
CREB1 0.014 0.02 -10000 0 -10000 0 0
IGFBP1 0.004 0.15 -10000 0 -0.56 5 5
PDX1 -0.061 0.2 -10000 0 -0.63 5 5
UCP2 -0.003 0.23 -10000 0 -0.87 5 5
ALDOB -0.009 0.26 -10000 0 -0.89 7 7
AFP -0.063 0.14 -10000 0 -0.44 15 15
BDH1 -0.002 0.23 -10000 0 -0.87 5 5
HADH 0.006 0.24 -10000 0 -0.86 5 5
F2 -0.01 0.26 -10000 0 -1.1 4 4
HNF1A -0.02 0.074 -10000 0 -0.51 4 4
G6PC -0.022 0.11 -10000 0 -0.51 3 3
SLC2A2 -0.007 0.18 -10000 0 -0.66 4 4
INS -0.008 0.025 -10000 0 -10000 0 0
FOXA1 -0.055 0.2 -10000 0 -0.57 33 33
FOXA3 -0.091 0.22 -10000 0 -0.48 57 57
FOXA2 -0.001 0.28 -10000 0 -0.94 6 6
ABCC8 -0.003 0.24 -10000 0 -0.9 5 5
ALB -0.071 0.16 -10000 0 -0.44 18 18
Nectin adhesion pathway

Figure S77.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S77.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.004 0.079 -9999 0 -0.57 5 5
alphaV beta3 Integrin -0.025 0.14 -9999 0 -0.42 29 29
PTK2 -0.044 0.12 -9999 0 -0.44 18 18
positive regulation of JNK cascade -0.022 0.076 -9999 0 -0.3 18 18
CDC42/GDP 0.028 0.12 -9999 0 -0.41 18 18
Rac1/GDP 0.03 0.12 -9999 0 -0.4 18 18
RAP1B 0.015 0 -9999 0 -10000 0 0
RAP1A 0.015 0 -9999 0 -10000 0 0
CTNNB1 0.015 0 -9999 0 -10000 0 0
CDC42/GTP -0.027 0.094 -9999 0 -0.37 18 18
nectin-3/I-afadin -0.009 0.11 -9999 0 -0.4 20 20
RAPGEF1 0.02 0.13 -9999 0 -0.45 18 18
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.011 0.15 -9999 0 -0.52 18 18
PDGFB-D/PDGFRB 0.004 0.079 -9999 0 -0.56 5 5
TLN1 0.016 0.068 -9999 0 -0.32 5 5
Rap1/GTP -0.022 0.08 -9999 0 -0.32 18 18
IQGAP1 0.015 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.029 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.009 0.11 -9999 0 -0.4 20 20
PVR 0.015 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.015 0 -9999 0 -10000 0 0
mol:GDP 0.021 0.15 -9999 0 -0.5 18 18
MLLT4 0.015 0 -9999 0 -10000 0 0
PIK3CA 0.015 0 -9999 0 -10000 0 0
PI3K 0.016 0.091 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.022 0 -9999 0 -10000 0 0
positive regulation of lamellipodium assembly -0.025 0.083 -9999 0 -0.31 20 20
PVRL1 0.015 0 -9999 0 -10000 0 0
PVRL3 -0.028 0.15 -9999 0 -0.56 20 20
PVRL2 0.015 0 -9999 0 -10000 0 0
PIK3R1 0.015 0 -9999 0 -10000 0 0
CDH1 -0.004 0.1 -9999 0 -0.57 9 9
CLDN1 -0.018 0.13 -9999 0 -0.54 16 16
JAM-A/CLDN1 -0.006 0.12 -9999 0 -0.32 28 28
SRC -0.044 0.15 -9999 0 -0.59 18 18
ITGB3 -0.048 0.18 -9999 0 -0.57 29 29
nectin-1(dimer)/I-afadin/I-afadin 0.022 0 -9999 0 -10000 0 0
FARP2 0.016 0.14 -9999 0 -0.5 18 18
RAC1 0.015 0 -9999 0 -10000 0 0
CTNNA1 0.015 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.004 0.095 -9999 0 -0.33 20 20
nectin-1/I-afadin 0.022 0 -9999 0 -10000 0 0
nectin-2/I-afadin 0.022 0 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.021 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.004 0.095 -9999 0 -0.33 20 20
CDC42/GTP/IQGAP1/filamentous actin 0.021 0 -9999 0 -10000 0 0
F11R 0.013 0.036 -9999 0 -0.57 1 1
positive regulation of filopodium formation -0.022 0.076 -9999 0 -0.3 18 18
alphaV/beta3 Integrin/Talin -0.001 0.13 -9999 0 -0.44 11 11
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.022 0 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.022 0 -9999 0 -10000 0 0
PIP5K1C 0.008 0.073 -9999 0 -0.35 5 5
VAV2 0.012 0.15 -9999 0 -0.5 20 20
RAP1/GDP -0.026 0.095 -9999 0 -0.37 18 18
ITGAV 0.013 0.036 -9999 0 -0.57 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.004 0.095 -9999 0 -0.33 20 20
nectin-3(dimer)/I-afadin/I-afadin -0.009 0.11 -9999 0 -0.4 20 20
Rac1/GTP -0.03 0.1 -9999 0 -0.38 20 20
PTPRM -0.002 0.08 -9999 0 -0.25 23 23
E-cadherin/beta catenin/alpha catenin -0.009 0.046 -9999 0 -10000 0 0
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.015 0 -9999 0 -10000 0 0
EGFR-dependent Endothelin signaling events

Figure S78.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S78.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.015 0 -9999 0 -10000 0 0
EGFR -0.007 0.11 -9999 0 -0.52 11 11
EGF/EGFR -0.061 0.12 -9999 0 -0.29 39 39
EGF/EGFR dimer/SHC/GRB2/SOS1 0.017 0.085 -9999 0 -0.46 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.057 0.19 -9999 0 -0.57 33 33
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.014 0.11 -9999 0 -0.48 15 15
EGF/EGFR dimer/SHC -0.002 0.098 -9999 0 -0.3 26 26
mol:GDP -0.023 0.071 -9999 0 -0.46 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.001 0.084 -9999 0 -0.51 7 7
GRB2/SOS1 0.022 0 -9999 0 -10000 0 0
HRAS/GTP -0.02 0.064 -9999 0 -0.42 1 1
SHC1 0.013 0.03 -9999 0 -0.48 1 1
HRAS/GDP -0.021 0.065 -9999 0 -0.43 1 1
FRAP1 0.014 0.08 -9999 0 -0.44 1 1
EGF/EGFR dimer -0.015 0.11 -9999 0 -0.35 26 26
SOS1 0.015 0 -9999 0 -10000 0 0
GRB2 0.015 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.04 0.15 -9999 0 -0.4 39 39
Regulation of nuclear SMAD2/3 signaling

Figure S79.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S79.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.016 0.006 -10000 0 -10000 0 0
HSPA8 0.015 0.002 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.067 0.15 0.22 2 -0.38 46 48
AKT1 0.015 0.014 -10000 0 -10000 0 0
GSC -0.004 0.078 -10000 0 -10000 0 0
NKX2-5 -0.072 0.18 -10000 0 -0.48 43 43
muscle cell differentiation 0.048 0.086 0.41 7 -10000 0 7
SMAD2-3/SMAD4/SP1 0.05 0.092 -10000 0 -0.4 3 3
SMAD4 0.011 0.05 -10000 0 -10000 0 0
CBFB 0.015 0 -10000 0 -10000 0 0
SAP18 0.015 0.001 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.026 0.043 -10000 0 -0.27 5 5
SMAD3/SMAD4/VDR -0.002 0.042 -10000 0 -0.48 1 1
MYC -0.012 0.13 -10000 0 -0.57 13 13
CDKN2B -0.01 0.25 -10000 0 -1.4 7 7
AP1 -0.044 0.19 -10000 0 -0.6 13 13
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.067 0.021 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.026 0.074 -10000 0 -0.33 4 4
SP3 0.018 0 -10000 0 -10000 0 0
CREB1 0.015 0 -10000 0 -10000 0 0
FOXH1 -0.098 0.21 -10000 0 -0.48 62 62
SMAD3/SMAD4/GR -0.019 0.079 -10000 0 -0.43 7 7
GATA3 -0.032 0.16 -10000 0 -0.56 20 20
SKI/SIN3/HDAC complex/NCoR1 0.053 0.008 -10000 0 -10000 0 0
MEF2C/TIF2 -0.064 0.2 -10000 0 -0.57 22 22
endothelial cell migration -0.005 0.13 1.4 2 -10000 0 2
MAX 0.013 0.004 -10000 0 -10000 0 0
RBBP7 0.015 0.001 -10000 0 -10000 0 0
RBBP4 0.015 0.001 -10000 0 -10000 0 0
RUNX2 0.005 0.07 -10000 0 -0.5 5 5
RUNX3 -0.007 0.11 -10000 0 -0.57 10 10
RUNX1 0.015 0 -10000 0 -10000 0 0
CTBP1 0.013 0.03 -10000 0 -0.48 1 1
NR3C1 -0.002 0.093 -10000 0 -0.57 7 7
VDR 0.011 0.047 -10000 0 -0.52 2 2
CDKN1A 0.054 0.11 -10000 0 -1.4 1 1
KAT2B 0.015 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.035 0.15 -10000 0 -0.37 19 19
DCP1A 0.015 0 -10000 0 -10000 0 0
SKI 0.015 0.001 -10000 0 -10000 0 0
SERPINE1 0.004 0.13 -10000 0 -1.4 2 2
SMAD3/SMAD4/ATF2 -0.006 0.045 -10000 0 -0.26 1 1
SMAD3/SMAD4/ATF3 -0.072 0.15 -10000 0 -0.39 48 48
SAP30 0.015 0.001 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.014 0.024 -10000 0 -10000 0 0
JUN -0.043 0.19 -10000 0 -0.59 13 13
SMAD3/SMAD4/IRF7 -0.02 0.079 -10000 0 -0.39 5 5
TFE3 0.022 0.013 -10000 0 -10000 0 0
COL1A2 -0.022 0.23 -10000 0 -1 12 12
mesenchymal cell differentiation 0.013 0.059 0.31 4 -10000 0 4
DLX1 -0.041 0.16 -10000 0 -0.48 29 29
TCF3 0.015 0 -10000 0 -10000 0 0
FOS -0.15 0.27 -10000 0 -0.56 80 80
SMAD3/SMAD4/Max -0.009 0.043 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.032 0.006 -10000 0 -10000 0 0
ZBTB17 0.016 0.012 -10000 0 -10000 0 0
LAMC1 0.045 0.065 -10000 0 -0.62 1 1
TGIF2/HDAC complex/SMAD3/SMAD4 -0.006 0.045 -10000 0 -10000 0 0
IRF7 -0.004 0.1 -10000 0 -0.51 10 10
ESR1 -0.086 0.22 -10000 0 -0.56 47 47
HNF4A -0.039 0.15 -10000 0 -0.48 27 27
MEF2C -0.059 0.18 -10000 0 -0.6 13 13
SMAD2-3/SMAD4 0.011 0.063 -10000 0 -0.32 1 1
Cbp/p300/Src-1 0.032 0.009 -10000 0 -10000 0 0
IGHV3OR16-13 -0.003 0.016 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.015 0 -10000 0 -10000 0 0
CREBBP 0.016 0.004 -10000 0 -10000 0 0
SKIL 0.013 0.03 -10000 0 -0.48 1 1
HDAC1 0.015 0.001 -10000 0 -10000 0 0
HDAC2 0.015 0.001 -10000 0 -10000 0 0
SNIP1 0.015 0.001 -10000 0 -10000 0 0
GCN5L2 0.001 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.036 0.066 -10000 0 -0.32 1 1
MSG1/HSC70 0.013 0.049 -10000 0 -0.34 5 5
SMAD2 0.018 0.018 -10000 0 -10000 0 0
SMAD3 0.01 0.046 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.035 0.046 -10000 0 -0.25 1 1
SMAD2/SMAD2/SMAD4 0.012 0.023 -10000 0 -10000 0 0
NCOR1 0.015 0.001 -10000 0 -10000 0 0
NCOA2 -0.02 0.14 -10000 0 -0.57 16 16
NCOA1 0.015 0 -10000 0 -10000 0 0
MYOD/E2A 0.011 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.063 0.086 -10000 0 -0.42 2 2
IFNB1 0.014 0.097 -10000 0 -0.45 6 6
SMAD3/SMAD4/MEF2C -0.057 0.18 -10000 0 -0.56 16 16
CITED1 0.006 0.068 -10000 0 -0.48 5 5
SMAD2-3/SMAD4/ARC105 0.035 0.063 -10000 0 -10000 0 0
RBL1 0.013 0.03 -10000 0 -0.48 1 1
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.042 0.1 -10000 0 -0.5 7 7
RUNX1-3/PEBPB2 0.017 0.07 -10000 0 -0.34 10 10
SMAD7 0.004 0.17 -10000 0 -0.55 10 10
MYC/MIZ-1 -0.01 0.096 -10000 0 -0.41 13 13
SMAD3/SMAD4 0.009 0.058 -10000 0 -0.41 2 2
IL10 -0.015 0.19 -10000 0 -0.61 19 19
PIASy/HDAC complex 0.014 0.005 -10000 0 -10000 0 0
PIAS3 0.015 0.002 -10000 0 -10000 0 0
CDK2 0.016 0.004 -10000 0 -10000 0 0
IL5 -0.004 0.13 -10000 0 -0.48 6 6
CDK4 0.016 0.004 -10000 0 -10000 0 0
PIAS4 0.014 0.005 -10000 0 -10000 0 0
ATF3 -0.089 0.22 -10000 0 -0.57 48 48
SMAD3/SMAD4/SP1 0.032 0.089 -10000 0 -0.36 6 6
FOXG1 -0.069 0.17 -10000 0 -0.48 39 39
FOXO3 0.026 0.019 -10000 0 -10000 0 0
FOXO1 0.026 0.019 -10000 0 -10000 0 0
FOXO4 0.024 0.029 -10000 0 -0.33 1 1
heart looping -0.058 0.18 -10000 0 -0.59 13 13
CEBPB 0.013 0.036 -10000 0 -0.56 1 1
SMAD3/SMAD4/DLX1 -0.039 0.1 -10000 0 -0.32 14 14
MYOD1 0 0 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 -0.035 0.097 -10000 0 -0.35 8 8
SMAD3/SMAD4/GATA3 -0.043 0.12 -10000 0 -0.38 23 23
SnoN/SIN3/HDAC complex/NCoR1 0.013 0.03 -10000 0 -0.48 1 1
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.025 0.087 -10000 0 -0.38 6 6
SMAD3/SMAD4/SP1-3 0.044 0.082 -10000 0 -0.34 3 3
MED15 0.015 0 -10000 0 -10000 0 0
SP1 0.02 0.03 -10000 0 -10000 0 0
SIN3B 0.015 0.001 -10000 0 -10000 0 0
SIN3A 0.015 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.066 0.17 -10000 0 -0.48 16 16
ITGB5 0.055 0.069 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.053 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.13 0.18 -10000 0 -0.36 91 91
AR -0.18 0.27 -10000 0 -0.57 90 90
negative regulation of cell growth 0.007 0.1 -10000 0 -0.41 4 4
SMAD3/SMAD4/MYOD -0.007 0.048 -10000 0 -0.28 1 1
E2F5 0.011 0.047 -10000 0 -0.52 2 2
E2F4 0.015 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.009 0.13 -10000 0 -0.37 8 8
SMAD2-3/SMAD4/FOXO1-3a-4 0.044 0.076 -10000 0 -0.34 7 7
TFDP1 0.015 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.042 0.19 -10000 0 -0.6 13 13
SMAD3/SMAD4/RUNX2 -0.012 0.06 -10000 0 -0.31 4 4
TGIF2 0.015 0 -10000 0 -10000 0 0
TGIF1 0.015 0 -10000 0 -10000 0 0
ATF2 0.015 0 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

Figure S80.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S80.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ANTXR1 0.015 0 -10000 0 -10000 0 0
ANTXR2 -0.013 0.12 -10000 0 -0.57 13 13
negative regulation of myeloid dendritic cell antigen processing and presentation -0.004 0.016 -10000 0 -0.074 13 13
monocyte activation -0.004 0.085 -10000 0 -0.41 11 11
MAP2K2 -0.001 0.006 -10000 0 -10000 0 0
MAP2K1 -0.003 0.013 -10000 0 -10000 0 0
MAP2K7 -0.003 0.013 -10000 0 -10000 0 0
MAP2K6 -0.007 0.037 -10000 0 -0.29 4 4
CYAA 0.002 0.067 -10000 0 -0.29 13 13
MAP2K4 -0.003 0.013 -10000 0 -10000 0 0
IL1B -0.015 0.09 -10000 0 -0.27 27 27
Channel 0.003 0.072 -10000 0 -0.32 13 13
NLRP1 -0.006 0.034 -10000 0 -0.3 3 3
CALM1 0.015 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.004 0.017 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.004 0.016 0.074 13 -10000 0 13
MAPK3 -0.003 0.013 -10000 0 -10000 0 0
MAPK1 -0.003 0.013 -10000 0 -10000 0 0
PGR -0.095 0.14 -10000 0 -0.31 81 81
PA/Cellular Receptors 0.003 0.079 -10000 0 -0.35 13 13
apoptosis -0.004 0.016 -10000 0 -0.074 13 13
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.004 0.068 -10000 0 -0.3 13 13
macrophage activation 0.018 0.015 -10000 0 -10000 0 0
TNF -0.009 0.11 -10000 0 -0.48 13 13
VCAM1 -0.004 0.086 -10000 0 -0.41 11 11
platelet activation -0.004 0.017 -10000 0 -10000 0 0
MAPKKK cascade -0.013 0.019 -10000 0 -10000 0 0
IL18 0.006 0.056 -10000 0 -0.33 6 6
negative regulation of macrophage activation -0.004 0.016 -10000 0 -0.074 13 13
LEF -0.004 0.016 -10000 0 -0.074 13 13
CASP1 -0.007 0.032 -10000 0 -0.18 6 6
mol:cAMP -0.004 0.017 -10000 0 -10000 0 0
necrosis -0.004 0.016 -10000 0 -0.074 13 13
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.004 0.068 -10000 0 -0.3 13 13
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
IL1-mediated signaling events

Figure S81.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S81.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.017 0.006 -10000 0 -10000 0 0
PRKCZ 0.013 0.036 -10000 0 -0.57 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.015 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.019 0.05 -10000 0 -0.28 2 2
IRAK/TOLLIP 0.033 0.004 -10000 0 -10000 0 0
IKBKB 0.015 0 -10000 0 -10000 0 0
IKBKG 0.015 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.095 0.19 -10000 0 -0.38 78 78
IL1A -0.088 0.21 -10000 0 -0.52 51 51
IL1B -0.026 0.14 -10000 0 -0.39 33 33
IRAK/TRAF6/p62/Atypical PKCs -0.001 0.014 -10000 0 -10000 0 0
IL1R2 -0.046 0.16 -10000 0 -0.49 32 32
IL1R1 0.013 0.036 -10000 0 -0.57 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.027 0.063 0.22 1 -0.4 1 2
TOLLIP 0.015 0 -10000 0 -10000 0 0
TICAM2 0.013 0.036 -10000 0 -0.57 1 1
MAP3K3 0.015 0 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.01 0 -10000 0 -10000 0 0
IKK complex/ELKS 0.073 0.007 -10000 0 -10000 0 0
JUN 0.036 0.061 -10000 0 -10000 0 0
MAP3K7 0.015 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.007 0.11 -10000 0 -0.49 4 4
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.029 0.13 -10000 0 -0.32 26 26
PIK3R1 0.015 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.019 0.13 -10000 0 -0.5 3 3
IL1 beta fragment/IL1R1/IL1RAP -0.011 0.12 -10000 0 -0.34 22 22
NFKB1 0.015 0 -10000 0 -10000 0 0
MAPK8 0.037 0.045 -10000 0 -10000 0 0
IRAK1 0.027 0.005 -10000 0 -10000 0 0
IL1RN/IL1R1 0.005 0.086 -10000 0 -0.38 12 12
IRAK4 0.015 0 -10000 0 -10000 0 0
PRKCI 0.015 0 -10000 0 -10000 0 0
TRAF6 0.015 0 -10000 0 -10000 0 0
PI3K 0.022 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.019 0.071 -10000 0 -0.37 2 2
CHUK 0.015 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.011 0.12 -10000 0 -0.34 22 22
IL1 beta/IL1R2 -0.05 0.16 -10000 0 -0.33 59 59
IRAK/TRAF6/TAK1/TAB1/TAB2 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.032 0.083 -10000 0 -0.44 4 4
IRAK3 0.002 0.086 -10000 0 -0.57 6 6
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.006 0.11 -10000 0 -0.49 4 4
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.002 0.092 -10000 0 -0.5 1 1
IL1 alpha/IL1R1/IL1RAP -0.043 0.15 -10000 0 -0.32 57 57
RELA 0.015 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.015 0 -10000 0 -10000 0 0
MYD88 0.015 0 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.042 0.004 -10000 0 -10000 0 0
IL1RAP 0 0.085 -10000 0 -0.48 8 8
UBE2N 0.015 0 -10000 0 -10000 0 0
IRAK/TRAF6 -0.029 0.076 -10000 0 -0.4 4 4
CASP1 -0.002 0.099 -10000 0 -0.57 8 8
IL1RN/IL1R2 -0.038 0.14 -10000 0 -0.36 42 42
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.001 0.12 -10000 0 -0.51 4 4
TMEM189-UBE2V1 0.008 0.008 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.015 0.077 -10000 0 -0.51 1 1
PIK3CA 0.015 0 -10000 0 -10000 0 0
IL1RN -0.008 0.11 -10000 0 -0.5 12 12
TRAF6/TAK1/TAB1/TAB2 0 0 -10000 0 -10000 0 0
MAP2K6 0.033 0.035 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

Figure S82.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S82.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.049 0.09 -10000 0 -0.57 2 2
UGCG -0.02 0.18 -10000 0 -0.69 16 16
AKT1/mTOR/p70S6K/Hsp90/TERT 0.024 0.12 -10000 0 -0.36 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.017 0.17 -10000 0 -0.68 16 16
mol:DAG 0 0.003 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.043 0.13 -10000 0 -0.4 26 26
FRAP1 0.036 0.18 -10000 0 -0.47 26 26
FOXO3 0.048 0.16 -10000 0 -0.47 16 16
AKT1 0.04 0.17 -10000 0 -0.47 20 20
GAB2 0.015 0.004 -10000 0 -10000 0 0
SMPD1 0.022 0.03 -10000 0 -10000 0 0
SGMS1 0.022 0.03 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.023 0.007 -10000 0 -10000 0 0
CALM1 0.015 0 -10000 0 -10000 0 0
cell proliferation 0.009 0.15 -10000 0 -0.35 28 28
EIF3A 0.015 0 -10000 0 -10000 0 0
PI3K 0.027 0.009 -10000 0 -10000 0 0
RPS6KB1 0.018 0.036 -10000 0 -10000 0 0
mol:sphingomyelin 0 0.003 -10000 0 -10000 0 0
natural killer cell activation 0 0.003 -10000 0 -0.012 10 10
JAK3 0.014 0.043 -10000 0 -0.48 2 2
PIK3R1 0.018 0.004 -10000 0 -10000 0 0
JAK1 0.018 0.004 -10000 0 -10000 0 0
NFKB1 0.015 0 -10000 0 -10000 0 0
MYC 0.021 0.25 -10000 0 -0.92 16 16
MYB -0.013 0.13 -10000 0 -1.3 1 1
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.043 0.14 -10000 0 -0.6 7 7
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.034 0.033 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.043 0.13 -10000 0 -0.58 7 7
Rac1/GDP 0.03 0.01 -10000 0 -10000 0 0
T cell proliferation 0.049 0.13 -10000 0 -0.58 6 6
SHC1 0.013 0.031 -10000 0 -0.48 1 1
RAC1 0.015 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.002 0.012 -10000 0 -0.03 33 33
PRKCZ 0.049 0.13 -10000 0 -0.61 6 6
NF kappa B1 p50/RelA -0.031 0.13 -10000 0 -0.44 19 19
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.042 0.096 -10000 0 -0.49 7 7
HSP90AA1 0.015 0 -10000 0 -10000 0 0
RELA 0.015 0 -10000 0 -10000 0 0
IL2RA -0.044 0.17 -10000 0 -0.53 29 29
IL2RB 0.007 0.079 -10000 0 -0.57 5 5
TERT -0.18 0.24 -10000 0 -0.48 106 106
E2F1 -0.003 0.079 -10000 0 -0.3 4 4
SOS1 0.015 0.004 -10000 0 -10000 0 0
RPS6 0.015 0 -10000 0 -10000 0 0
mol:cAMP -0.001 0.006 0.014 33 -10000 0 33
PTPN11 0.015 0.004 -10000 0 -10000 0 0
IL2RG -0.009 0.12 -10000 0 -0.53 13 13
actin cytoskeleton organization 0.049 0.13 -10000 0 -0.58 6 6
GRB2 0.015 0.004 -10000 0 -10000 0 0
IL2 0.007 0.008 -10000 0 -10000 0 0
PIK3CA 0.018 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.038 0.013 -10000 0 -10000 0 0
LCK 0.007 0.077 -10000 0 -0.55 5 5
BCL2 0.025 0.23 -10000 0 -0.78 17 17
a4b1 and a4b7 Integrin signaling

Figure S83.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S83.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.015 0 -9999 0 -10000 0 0
ITGB7 0.006 0.071 -9999 0 -0.57 4 4
ITGA4 -0.006 0.11 -9999 0 -0.56 10 10
alpha4/beta7 Integrin 0 0.094 -9999 0 -0.4 14 14
alpha4/beta1 Integrin 0.007 0.08 -9999 0 -0.4 10 10
Signaling events mediated by PTP1B

Figure S84.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S84.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.004 0.079 -10000 0 -0.57 5 5
Jak2/Leptin Receptor -0.002 0.089 0.2 11 -0.37 5 16
PTP1B/AKT1 0.027 0.047 -10000 0 -10000 0 0
FYN 0.009 0.061 -10000 0 -0.57 3 3
p210 bcr-abl/PTP1B 0.021 0.052 -10000 0 -0.27 2 2
EGFR -0.006 0.11 -10000 0 -0.52 11 11
EGF/EGFR -0.023 0.067 -10000 0 -0.29 7 7
CSF1 -0.011 0.12 -10000 0 -0.57 12 12
AKT1 0.016 0.001 -10000 0 -10000 0 0
INSR 0.016 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin 0.001 0.094 -10000 0 -0.26 16 16
Insulin Receptor/Insulin -0.003 0.025 -10000 0 -10000 0 0
HCK -0.01 0.12 -10000 0 -0.55 12 12
CRK 0.015 0 -10000 0 -10000 0 0
TYK2 0.028 0.049 -10000 0 -0.25 2 2
EGF -0.013 0.11 -10000 0 -0.48 15 15
YES1 0.015 0 -10000 0 -10000 0 0
CAV1 0.025 0.064 -10000 0 -0.26 3 3
TXN 0.014 0.031 -10000 0 -0.48 1 1
PTP1B/IRS1/GRB2 0.029 0.068 -10000 0 -0.34 4 4
cell migration -0.021 0.052 0.27 2 -10000 0 2
STAT3 0.015 0.001 -10000 0 -10000 0 0
PRLR -0.041 0.16 -10000 0 -0.51 29 29
ITGA2B -0.025 0.13 -10000 0 -0.48 21 21
CSF1R -0.021 0.14 -10000 0 -0.56 17 17
Prolactin Receptor/Prolactin -0.038 0.12 -10000 0 -0.36 33 33
FGR 0.013 0.036 -10000 0 -0.57 1 1
PTP1B/p130 Cas 0.028 0.049 -10000 0 -0.25 2 2
Crk/p130 Cas 0.036 0.047 -10000 0 -10000 0 0
DOK1 0.03 0.06 -10000 0 -0.27 4 4
JAK2 0.013 0.071 -10000 0 -0.31 5 5
Jak2/Leptin Receptor/Leptin -0.07 0.14 -10000 0 -0.42 29 29
PIK3R1 0.015 0 -10000 0 -10000 0 0
PTPN1 0.021 0.052 -10000 0 -0.27 2 2
LYN 0.015 0 -10000 0 -10000 0 0
CDH2 -0.038 0.16 -10000 0 -0.49 28 28
SRC 0.028 0.022 -10000 0 -10000 0 0
ITGB3 -0.048 0.18 -10000 0 -0.57 29 29
CAT1/PTP1B -0.003 0.11 -10000 0 -0.36 9 9
CAPN1 0.016 0.002 -10000 0 -10000 0 0
CSK 0.015 0 -10000 0 -10000 0 0
PI3K -0.001 0.021 -10000 0 -10000 0 0
mol:H2O2 0 0.003 -10000 0 -10000 0 0
STAT3 (dimer) -0.069 0.15 -10000 0 -0.45 28 28
negative regulation of transcription 0.017 0.072 -10000 0 -0.3 5 5
FCGR2A -0.004 0.096 -10000 0 -0.49 10 10
FER 0.013 0.036 -10000 0 -0.57 1 1
alphaIIb/beta3 Integrin -0.055 0.16 -10000 0 -0.4 46 46
BLK -0.056 0.18 -10000 0 -0.54 33 33
Insulin Receptor/Insulin/Shc 0.02 0.019 -10000 0 -0.29 1 1
RHOA 0.016 0.002 -10000 0 -10000 0 0
LEPR -0.002 0.098 -10000 0 -0.56 8 8
BCAR1 0.015 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.015 0 -10000 0 -10000 0 0
mol:NADPH 0.001 0.002 -10000 0 -10000 0 0
TRPV6 -0.026 0.13 -10000 0 -0.44 11 11
PRL -0.001 0.06 -10000 0 -0.48 4 4
SOCS3 -0.14 0.43 -10000 0 -1.4 28 28
SPRY2 0 0.094 -10000 0 -0.57 7 7
Insulin Receptor/Insulin/IRS1 0.013 0.055 -10000 0 -0.35 6 6
CSF1/CSF1R 0.004 0.12 -10000 0 -0.36 16 16
Ras protein signal transduction 0.01 0.017 -10000 0 -10000 0 0
IRS1 0.002 0.086 -10000 0 -0.57 6 6
INS 0.001 0.001 -10000 0 -10000 0 0
LEP -0.059 0.18 -10000 0 -0.54 34 34
STAT5B 0.024 0.053 -10000 0 -0.24 3 3
STAT5A 0.023 0.054 -10000 0 -0.24 3 3
GRB2 0.015 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.022 0.068 -10000 0 -0.3 7 7
CSN2 -0.012 0.045 -10000 0 -10000 0 0
PIK3CA 0.015 0 -10000 0 -10000 0 0
LAT 0.023 0.036 -10000 0 -0.39 1 1
YBX1 0.023 0.03 -10000 0 -0.46 1 1
LCK 0.005 0.077 -10000 0 -0.55 5 5
SHC1 0.013 0.03 -10000 0 -0.48 1 1
NOX4 -0.013 0.11 -10000 0 -0.48 15 15
Ephrin B reverse signaling

Figure S85.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S85.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.015 0 -10000 0 -10000 0 0
EPHB2 -0.014 0.12 -10000 0 -0.48 16 16
EFNB1 0.017 0.059 -10000 0 -0.41 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.028 0.095 -10000 0 -0.51 3 3
Ephrin B2/EPHB1-2 -0.011 0.1 -10000 0 -0.28 36 36
neuron projection morphogenesis -0.034 0.087 -10000 0 -0.48 3 3
Ephrin B1/EPHB1-2/Tiam1 0 0.12 -10000 0 -0.36 9 9
DNM1 0.004 0.079 -10000 0 -0.57 5 5
cell-cell signaling 0.001 0.001 -10000 0 -10000 0 0
MAP2K4 0.012 0.096 -10000 0 -0.61 6 6
YES1 -0.017 0.13 -10000 0 -0.86 6 6
Ephrin B1/EPHB1-2/NCK2 0.001 0.11 -10000 0 -0.36 7 7
PI3K 0.014 0.097 -10000 0 -0.62 6 6
mol:GDP -0.001 0.11 -10000 0 -0.36 9 9
ITGA2B -0.024 0.13 -10000 0 -0.48 21 21
endothelial cell proliferation 0.019 0.005 -10000 0 -10000 0 0
FYN -0.019 0.13 -10000 0 -0.89 6 6
MAP3K7 -0.01 0.099 -10000 0 -0.66 6 6
FGR -0.017 0.13 -10000 0 -0.88 6 6
TIAM1 0.013 0.036 -10000 0 -0.57 1 1
PIK3R1 0.015 0 -10000 0 -10000 0 0
RGS3 0.015 0 -10000 0 -10000 0 0
cell adhesion -0.022 0.14 -10000 0 -0.53 10 10
LYN -0.017 0.13 -10000 0 -0.86 6 6
Ephrin B1/EPHB1-2/Src Family Kinases -0.018 0.12 -10000 0 -0.81 6 6
Ephrin B1/EPHB1-2 -0.017 0.11 -10000 0 -0.71 6 6
SRC -0.017 0.13 -10000 0 -0.86 6 6
ITGB3 -0.048 0.18 -10000 0 -0.57 29 29
EPHB1 -0.028 0.15 -10000 0 -0.56 20 20
EPHB4 0.015 0 -10000 0 -10000 0 0
RAC1 0.015 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.02 0.005 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.051 0.17 -10000 0 -0.4 46 46
BLK -0.033 0.13 -10000 0 -0.86 6 6
HCK -0.023 0.13 -10000 0 -0.88 6 6
regulation of stress fiber formation 0 0.11 0.37 6 -10000 0 6
MAPK8 0.017 0.11 -10000 0 -0.67 6 6
Ephrin B1/EPHB1-2/RGS3 0.001 0.11 -10000 0 -0.36 7 7
endothelial cell migration -0.008 0.083 -10000 0 -0.55 6 6
NCK2 0.015 0 -10000 0 -10000 0 0
PTPN13 -0.009 0.1 -10000 0 -0.68 6 6
regulation of focal adhesion formation 0 0.11 0.37 6 -10000 0 6
chemotaxis 0 0.11 0.35 7 -10000 0 7
PIK3CA 0.015 0 -10000 0 -10000 0 0
Rac1/GTP -0.035 0.089 -10000 0 -0.5 3 3
angiogenesis -0.017 0.1 -10000 0 -0.71 6 6
LCK -0.019 0.13 -10000 0 -0.86 6 6
Role of Calcineurin-dependent NFAT signaling in lymphocytes

Figure S86.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S86.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.013 0.03 -10000 0 -0.48 1 1
NFATC1 0.034 0.077 -10000 0 -0.3 10 10
NFATC2 -0.025 0.078 -10000 0 -0.2 31 31
NFATC3 0.011 0.029 -10000 0 -0.41 1 1
YWHAE 0.013 0.036 -10000 0 -0.57 1 1
Calcineurin A alpha-beta B1/CABIN1 -0.044 0.14 -10000 0 -0.44 21 21
Exportin 1/Ran/NUP214 0.014 0.016 -10000 0 -10000 0 0
mol:DAG -0.003 0.003 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.071 0.12 -10000 0 -0.41 25 25
BCL2/BAX 0.003 0.089 -10000 0 -0.41 12 12
CaM/Ca2+/Calcineurin A alpha-beta B1 0.003 0.01 -10000 0 -10000 0 0
CaM/Ca2+ 0.003 0.01 -10000 0 -10000 0 0
BAX 0.015 0 -10000 0 -10000 0 0
MAPK14 0.007 0.008 -10000 0 -10000 0 0
BAD 0.015 0 -10000 0 -10000 0 0
CABIN1/MEF2D -0.039 0.14 -10000 0 -0.42 20 20
Calcineurin A alpha-beta B1/BCL2 -0.011 0.12 -10000 0 -0.56 12 12
FKBP8 0.015 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.038 0.14 0.42 20 -10000 0 20
KPNB1 0.015 0 -10000 0 -10000 0 0
KPNA2 0.011 0.043 -10000 0 -0.48 2 2
XPO1 0.014 0.001 -10000 0 -10000 0 0
SFN -0.036 0.15 -10000 0 -0.49 27 27
MAP3K8 0.001 0.061 -10000 0 -0.57 3 3
NFAT4/CK1 alpha -0.001 0.015 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.13 0.18 -10000 0 -0.39 31 31
CABIN1 -0.045 0.14 -10000 0 -0.44 21 21
CALM1 0.01 0.006 -10000 0 -10000 0 0
RAN 0.014 0.001 -10000 0 -10000 0 0
MAP3K1 0.015 0 -10000 0 -10000 0 0
CAMK4 -0.007 0.11 -10000 0 -0.56 10 10
mol:Ca2+ -0.009 0.009 -10000 0 -10000 0 0
MAPK3 0.015 0 -10000 0 -10000 0 0
YWHAH 0.015 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.006 0.038 -10000 0 -0.34 3 3
YWHAB 0.015 0 -10000 0 -10000 0 0
MAPK8 0.001 0.061 -10000 0 -0.57 3 3
MAPK9 0.015 0 -10000 0 -10000 0 0
YWHAG 0.015 0 -10000 0 -10000 0 0
FKBP1A 0.015 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.027 0.081 -10000 0 -0.35 2 2
PRKCH 0.015 0 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.009 0.014 -10000 0 -10000 0 0
CASP3 0.007 0.008 -10000 0 -10000 0 0
PIM1 0.015 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.005 0.006 -10000 0 -10000 0 0
apoptosis -0.006 0.026 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.034 0.036 -10000 0 -0.27 1 1
PRKCB -0.15 0.26 -10000 0 -0.57 75 75
PRKCE 0.015 0 -10000 0 -10000 0 0
JNK2/NFAT4 0.024 0.025 -10000 0 -0.37 1 1
BAD/BCL-XL 0.021 0.022 -10000 0 -0.34 1 1
PRKCD 0.015 0 -10000 0 -10000 0 0
NUP214 0.014 0.001 -10000 0 -10000 0 0
PRKCZ 0.005 0.036 -10000 0 -0.57 1 1
PRKCA 0.013 0.036 -10000 0 -0.57 1 1
PRKCG -0.005 0.079 -10000 0 -0.48 7 7
PRKCQ -0.045 0.18 -10000 0 -0.56 28 28
FKBP38/BCL2 0.003 0.089 -10000 0 -0.41 12 12
EP300 0.009 0.006 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.015 0 -10000 0 -10000 0 0
NFATc/JNK1 0.014 0.08 -10000 0 -10000 0 0
CaM/Ca2+/FKBP38 0.01 0.011 -10000 0 -10000 0 0
FKBP12/FK506 0.011 0 -10000 0 -10000 0 0
CSNK1A1 0.01 0.012 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.003 0.069 -10000 0 -0.35 10 10
NFATc/ERK1 0.042 0.074 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.068 0.12 -10000 0 -0.4 25 25
NR4A1 -0.27 0.3 -10000 0 -0.54 147 147
GSK3B 0.007 0.008 -10000 0 -10000 0 0
positive T cell selection 0.011 0.029 -10000 0 -0.41 1 1
NFAT1/CK1 alpha -0.035 0.052 -10000 0 -0.29 3 3
RCH1/ KPNB1 0.02 0.031 -10000 0 -0.34 2 2
YWHAQ 0.015 0 -10000 0 -10000 0 0
PRKACA 0.007 0.008 -10000 0 -10000 0 0
AKAP5 0.009 0.053 -10000 0 -0.48 3 3
MEF2D 0.009 0.006 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.015 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.017 0.076 -10000 0 -10000 0 0
CREBBP 0.009 0.006 -10000 0 -10000 0 0
BCL2 -0.011 0.12 -10000 0 -0.57 12 12
Syndecan-3-mediated signaling events

Figure S87.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S87.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.013 0.03 -9999 0 -0.48 1 1
Syndecan-3/Src/Cortactin -0.066 0.11 -9999 0 -0.8 1 1
Syndecan-3/Neurocan -0.011 0.055 -9999 0 -0.59 1 1
POMC -0.011 0.12 -9999 0 -0.52 13 13
EGFR -0.007 0.11 -9999 0 -0.52 11 11
Syndecan-3/EGFR -0.012 0.061 -9999 0 -0.33 6 6
AGRP 0.009 0.007 -9999 0 -10000 0 0
NCSTN 0.015 0 -9999 0 -10000 0 0
PSENEN 0.015 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.015 0 -9999 0 -10000 0 0
APH1A 0.015 0 -9999 0 -10000 0 0
NCAN -0.01 0.094 -9999 0 -0.48 10 10
long-term memory -0.006 0.055 -9999 0 -0.8 1 1
Syndecan-3/IL8 -0.044 0.11 -9999 0 -0.29 40 40
PSEN1 0.015 0 -9999 0 -10000 0 0
Src/Cortactin 0.021 0.022 -9999 0 -0.34 1 1
FYN 0.009 0.061 -9999 0 -0.57 3 3
limb bud formation -0.002 0.038 -9999 0 -0.61 1 1
MC4R -0.002 0.06 -9999 0 -0.48 4 4
SRC 0.015 0 -9999 0 -10000 0 0
PTN -0.14 0.25 -9999 0 -0.55 71 71
FGFR/FGF/Syndecan-3 -0.002 0.038 -9999 0 -0.62 1 1
neuron projection morphogenesis -0.048 0.13 -9999 0 -0.58 2 2
Syndecan-3/AgRP -0.002 0.036 -9999 0 -0.59 1 1
Syndecan-3/AgRP/MC4R 0.002 0.046 -9999 0 -0.57 1 1
Fyn/Cortactin 0.016 0.05 -9999 0 -0.39 4 4
SDC3 -0.002 0.038 -9999 0 -0.63 1 1
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.044 0.11 -9999 0 -0.29 40 40
IL8 -0.074 0.21 -9999 0 -0.56 41 41
Syndecan-3/Fyn/Cortactin 0.031 0.061 -9999 0 -0.84 1 1
Syndecan-3/CASK -0.002 0.037 -9999 0 -0.6 1 1
alpha-MSH/MC4R -0.009 0.093 -9999 0 -0.36 17 17
Gamma Secretase 0.045 0 -9999 0 -10000 0 0
Regulation of p38-alpha and p38-beta

Figure S88.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S88.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
RIP1/MEKK3 0.021 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.015 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.007 0.068 -9999 0 -0.55 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.015 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.024 0.023 -9999 0 -0.21 1 1
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.015 0 -9999 0 -10000 0 0
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.015 0 -9999 0 -10000 0 0
FYN 0.009 0.061 -9999 0 -0.57 3 3
MAP3K12 0.013 0.036 -9999 0 -0.57 1 1
FGR 0.013 0.036 -9999 0 -0.57 1 1
p38 alpha/TAB1 -0.021 0.053 -9999 0 -0.27 7 7
PRKG1 -0.11 0.24 -9999 0 -0.57 58 58
DUSP8 -0.024 0.15 -9999 0 -0.57 18 18
PGK/cGMP/p38 alpha -0.069 0.12 -9999 0 -0.33 30 30
apoptosis -0.02 0.051 -9999 0 -0.26 7 7
RAL/GTP 0.021 0 -9999 0 -10000 0 0
LYN 0.015 0 -9999 0 -10000 0 0
DUSP1 -0.15 0.26 -9999 0 -0.57 76 76
PAK1 0.013 0.036 -9999 0 -0.57 1 1
SRC 0.015 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.038 0.017 -9999 0 -0.24 1 1
TRAF6 0.015 0 -9999 0 -10000 0 0
RAC1 0.015 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0.013 0.03 -9999 0 -0.48 1 1
RAC1-CDC42/GTP 0.021 0 -9999 0 -10000 0 0
MAPK11 0.025 0.097 -9999 0 -0.33 8 8
BLK -0.056 0.18 -9999 0 -0.54 33 33
HCK -0.01 0.12 -9999 0 -0.55 12 12
MAP2K3 0.015 0 -9999 0 -10000 0 0
DUSP16 0.015 0 -9999 0 -10000 0 0
DUSP10 0.008 0.061 -9999 0 -0.48 4 4
TRAF6/MEKK3 0.02 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.03 0.08 -9999 0 -0.29 7 7
positive regulation of innate immune response 0.033 0.11 -9999 0 -0.36 8 8
LCK 0.005 0.077 -9999 0 -0.55 5 5
p38alpha-beta/MKP7 0.039 0.1 -9999 0 -0.35 7 7
p38alpha-beta/MKP5 0.036 0.11 -9999 0 -0.38 5 5
PGK/cGMP -0.082 0.18 -9999 0 -0.42 58 58
PAK2 0.015 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.035 0.17 -9999 0 -0.41 28 28
CDC42 0.015 0 -9999 0 -10000 0 0
RALB 0.015 0 -9999 0 -10000 0 0
RALA 0.015 0 -9999 0 -10000 0 0
PAK3 -0.006 0.084 -9999 0 -0.48 8 8
Class I PI3K signaling events mediated by Akt

Figure S89.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S89.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.024 0.022 -9999 0 -0.34 1 1
BAD/BCL-XL/YWHAZ 0.037 0.017 -9999 0 -10000 0 0
CDKN1B 0.042 0 -9999 0 -10000 0 0
CDKN1A 0.041 0.018 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
PRKDC 0.015 0 -9999 0 -10000 0 0
FOXO3 0.042 0 -9999 0 -10000 0 0
AKT1 0 0 -9999 0 -10000 0 0
BAD 0.015 0 -9999 0 -10000 0 0
AKT3 0.006 0.069 -9999 0 -0.34 10 10
mol:GTP 0 0 -9999 0 -10000 0 0
FOXO4 0.041 0.015 -9999 0 -10000 0 0
AKT1/ASK1 0.04 0 -9999 0 -10000 0 0
BAD/YWHAZ 0.031 0 -9999 0 -10000 0 0
RICTOR 0.015 0 -9999 0 -10000 0 0
RAF1 0.013 0.03 -9999 0 -0.48 1 1
JNK cascade 0 0 -9999 0 -10000 0 0
TSC1 0.042 0 -9999 0 -10000 0 0
YWHAZ 0.015 0 -9999 0 -10000 0 0
AKT1/RAF1 0.041 0.015 -9999 0 -10000 0 0
EP300 0.015 0 -9999 0 -10000 0 0
mol:GDP 0.035 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -10000 0 0
TSC2 0.042 0 -9999 0 -10000 0 0
YWHAQ 0.015 0 -9999 0 -10000 0 0
TBC1D4 0.027 0 -9999 0 -10000 0 0
MAP3K5 0.015 0 -9999 0 -10000 0 0
MAPKAP1 0.015 0 -9999 0 -10000 0 0
negative regulation of cell cycle -0.042 0.026 -9999 0 -10000 0 0
YWHAH 0.015 0 -9999 0 -10000 0 0
AKT1S1 0.042 0 -9999 0 -10000 0 0
CASP9 0.042 0 -9999 0 -10000 0 0
YWHAB 0.015 0 -9999 0 -10000 0 0
p27Kip1/KPNA1 0.049 0 -9999 0 -10000 0 0
GBL 0 0 -9999 0 -10000 0 0
PDK1/Src/Hsp90 0.031 0 -9999 0 -10000 0 0
YWHAE 0.013 0.036 -9999 0 -0.57 1 1
SRC 0.015 0 -9999 0 -10000 0 0
AKT2/p21CIP1 -0.001 0.015 -9999 0 -10000 0 0
KIAA1303 0 0 -9999 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.021 0 -9999 0 -10000 0 0
CHUK 0.042 0 -9999 0 -10000 0 0
BAD/BCL-XL 0.056 0.014 -9999 0 -10000 0 0
mTORC2 0.02 0 -9999 0 -10000 0 0
AKT2 0.02 0 -9999 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.059 0.029 -9999 0 -10000 0 0
PDPK1 0.015 0 -9999 0 -10000 0 0
MDM2 0.035 0.042 -9999 0 -10000 0 0
MAPKKK cascade -0.041 0.015 -9999 0 -10000 0 0
MDM2/Cbp/p300 0.049 0.039 -9999 0 -10000 0 0
TSC1/TSC2 0.049 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.047 0.038 -9999 0 -10000 0 0
glucose import -0.21 0.15 -9999 0 -0.3 195 195
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.036 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
SLC2A4 -0.21 0.15 -9999 0 -0.3 195 195
GSK3A 0.042 0 -9999 0 -10000 0 0
FOXO1 0.042 0 -9999 0 -10000 0 0
GSK3B 0.042 0 -9999 0 -10000 0 0
SFN -0.036 0.15 -9999 0 -0.49 27 27
G1/S transition of mitotic cell cycle 0.049 0 -9999 0 -10000 0 0
p27Kip1/14-3-3 family 0.043 0.039 -9999 0 -0.28 1 1
PRKACA 0.015 0 -9999 0 -10000 0 0
KPNA1 0.015 0 -9999 0 -10000 0 0
HSP90AA1 0.015 0 -9999 0 -10000 0 0
YWHAG 0.015 0 -9999 0 -10000 0 0
RHEB 0.015 0 -9999 0 -10000 0 0
CREBBP 0.015 0 -9999 0 -10000 0 0
Ceramide signaling pathway

Figure S90.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S90.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.024 0.022 -10000 0 -0.34 1 1
MAP4K4 0.036 0.058 -10000 0 -10000 0 0
BAG4 0.015 0 -10000 0 -10000 0 0
PKC zeta/ceramide -0.004 0.025 -10000 0 -0.31 1 1
NFKBIA 0.015 0 -10000 0 -10000 0 0
BIRC3 -0.019 0.14 -10000 0 -0.56 16 16
BAX 0.002 0.008 -10000 0 -10000 0 0
RIPK1 0.015 0 -10000 0 -10000 0 0
AKT1 0.021 0.005 -10000 0 -10000 0 0
BAD -0.004 0.017 -10000 0 -10000 0 0
SMPD1 0.025 0.029 -10000 0 -10000 0 0
RB1 -0.004 0.017 -10000 0 -10000 0 0
FADD/Caspase 8 0.044 0.063 -10000 0 -10000 0 0
MAP2K4 0.004 0.016 -10000 0 -10000 0 0
NSMAF 0.015 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.003 0.024 -10000 0 -0.29 1 1
EGF -0.014 0.11 -10000 0 -0.48 15 15
mol:ceramide -0.014 0.018 0.14 1 -10000 0 1
MADD 0.015 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.026 0 -10000 0 -10000 0 0
ASAH1 0.015 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.004 0.016 -10000 0 -10000 0 0
cell proliferation -0.088 0.13 -10000 0 -0.23 121 121
BID 0.03 0.039 -10000 0 -10000 0 0
MAP3K1 -0.004 0.017 -10000 0 -10000 0 0
EIF2A 0.012 0.015 -10000 0 -10000 0 0
TRADD 0.015 0 -10000 0 -10000 0 0
CRADD 0.015 0 -10000 0 -10000 0 0
MAPK3 0.016 0.022 -10000 0 -0.26 1 1
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.016 0.022 -10000 0 -0.26 1 1
Cathepsin D/ceramide -0.002 0.017 -10000 0 -10000 0 0
FADD 0.033 0.067 -10000 0 -0.3 2 2
KSR1 -0.004 0.017 -10000 0 -10000 0 0
MAPK8 0.006 0.033 -10000 0 -0.23 4 4
PRKRA -0.004 0.017 -10000 0 -10000 0 0
PDGFA 0.015 0 -10000 0 -10000 0 0
TRAF2 0.015 0 -10000 0 -10000 0 0
IGF1 -0.25 0.29 -10000 0 -0.57 121 121
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.014 0.018 0.14 1 -10000 0 1
CTSD 0.015 0 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.022 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.093 0.14 -10000 0 -0.24 121 121
PRKCD 0.015 0 -10000 0 -10000 0 0
PRKCZ 0.013 0.036 -10000 0 -0.57 1 1
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.026 0 -10000 0 -10000 0 0
RelA/NF kappa B1 0.022 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.013 0.036 -10000 0 -0.57 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.03 0.059 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.016 0.066 -10000 0 -0.27 13 13
mol:Sphingosine-1-phosphate 0.024 0.022 -10000 0 -0.34 1 1
MAP2K1 0.011 0.023 -10000 0 -0.27 1 1
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.015 0 -10000 0 -10000 0 0
CYCS 0.007 0.035 0.16 12 -10000 0 12
TNFRSF1A 0.015 0 -10000 0 -10000 0 0
NFKB1 0.015 0 -10000 0 -10000 0 0
TNFR1A/BAG4 0.022 0 -10000 0 -10000 0 0
EIF2AK2 0.004 0.016 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN 0.016 0.066 -10000 0 -0.27 13 13
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.04 0.035 -10000 0 -10000 0 0
MAP2K2 0.011 0.023 -10000 0 -0.27 1 1
SMPD3 0.027 0.032 -10000 0 -10000 0 0
TNF -0.009 0.11 -10000 0 -0.48 13 13
PKC zeta/PAR4 0.019 0.037 -10000 0 -0.41 2 2
mol:PHOSPHOCHOLINE -0.003 0.033 0.13 12 -10000 0 12
NF kappa B1/RelA/I kappa B alpha 0.043 0.027 -10000 0 -10000 0 0
AIFM1 0.007 0.035 0.16 12 -10000 0 12
BCL2 -0.011 0.12 -10000 0 -0.57 12 12
Paxillin-independent events mediated by a4b1 and a4b7

Figure S91.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S91.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.015 0.085 -9999 0 -0.35 13 13
CRKL 0.011 0.043 -9999 0 -0.48 2 2
Rac1/GDP 0.011 0 -9999 0 -10000 0 0
DOCK1 0.013 0.036 -9999 0 -0.57 1 1
ITGA4 -0.006 0.11 -9999 0 -0.56 10 10
alpha4/beta7 Integrin/MAdCAM1 0.01 0.095 -9999 0 -0.34 13 13
EPO -0.033 0.14 -9999 0 -0.48 24 24
alpha4/beta7 Integrin 0 0.094 -9999 0 -0.4 14 14
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.015 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.007 0.08 -9999 0 -0.4 10 10
EPO/EPOR (dimer) -0.021 0.11 -9999 0 -0.34 31 31
lamellipodium assembly 0.002 0.012 -9999 0 -10000 0 0
PIK3CA 0.015 0 -9999 0 -10000 0 0
PI3K 0.022 0 -9999 0 -10000 0 0
ARF6 0.015 0 -9999 0 -10000 0 0
JAK2 0.006 0.082 -9999 0 -0.3 10 10
PXN 0.015 0 -9999 0 -10000 0 0
PIK3R1 0.015 0 -9999 0 -10000 0 0
MADCAM1 -0.006 0.094 -9999 0 -0.48 10 10
cell adhesion 0.009 0.095 -9999 0 -0.34 13 13
CRKL/CBL 0.02 0.031 -9999 0 -0.34 2 2
ITGB1 0.015 0 -9999 0 -10000 0 0
SRC 0.012 0.1 -9999 0 -0.36 17 17
ITGB7 0.006 0.071 -9999 0 -0.57 4 4
RAC1 0.015 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.003 0.11 -9999 0 -0.41 17 17
p130Cas/Crk/Dock1 0.035 0.092 -9999 0 -0.5 4 4
VCAM1 -0.009 0.12 -9999 0 -0.57 11 11
RHOA 0.015 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.027 0.063 -9999 0 -0.3 9 9
BCAR1 0.021 0.098 -9999 0 -0.34 16 16
EPOR 0.002 0.08 -9999 0 -0.48 7 7
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.015 0 -9999 0 -10000 0 0
GIT1 0.015 0 -9999 0 -10000 0 0
Rac1/GTP 0.002 0.012 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class III

Figure S92.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S92.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.015 0 -10000 0 -10000 0 0
HDAC4 0.015 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.004 0.095 0.34 20 -10000 0 20
CDKN1A -0.003 0.046 -10000 0 -0.76 1 1
KAT2B 0.015 0 -10000 0 -10000 0 0
BAX 0.015 0 -10000 0 -10000 0 0
FOXO3 0 0 -10000 0 -10000 0 0
FOXO1 0.015 0 -10000 0 -10000 0 0
FOXO4 0.025 0.009 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.015 0 -10000 0 -10000 0 0
TAT -0.007 0.089 -10000 0 -0.48 9 9
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.013 0 -10000 0 -10000 0 0
PPARGC1A -0.22 0.28 -10000 0 -0.56 107 107
FHL2 0.013 0.036 -10000 0 -0.57 1 1
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.001 0.009 -10000 0 -10000 0 0
HIST2H4A -0.004 0.095 -10000 0 -0.34 20 20
SIRT1/FOXO3a 0.001 0.008 -10000 0 -10000 0 0
SIRT1 0.001 0.012 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.001 0.009 -10000 0 -10000 0 0
SIRT1/Histone H1b -0.01 0.031 -10000 0 -10000 0 0
apoptosis -0.001 0.009 -10000 0 -10000 0 0
SIRT1/PGC1A -0.14 0.17 -10000 0 -0.35 107 107
p53/SIRT1 0.002 0.025 0.4 1 -10000 0 1
SIRT1/FOXO4 0 0.012 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 -0.001 0.021 -10000 0 -0.31 1 1
HIST1H1E 0.01 0.046 -10000 0 -10000 0 0
SIRT1/p300 0.001 0.009 -10000 0 -10000 0 0
muscle cell differentiation -0.001 0.009 -10000 0 -10000 0 0
TP53 0.001 0.012 0.2 1 -10000 0 1
KU70/SIRT1/BAX 0.001 0.009 -10000 0 -10000 0 0
CREBBP 0.015 0 -10000 0 -10000 0 0
MEF2D 0.015 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.011 0.062 -10000 0 -0.34 9 9
ACSS2 0.022 0.023 -10000 0 -0.34 1 1
SIRT1/PCAF/MYOD 0.001 0.009 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

Figure S93.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S93.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
adherens junction organization 0.026 0.05 -10000 0 -0.24 9 9
epithelial cell differentiation -0.009 0.05 -10000 0 -0.28 9 9
CYFIP2 -0.002 0.099 -10000 0 -0.57 8 8
ENAH 0.059 0.054 -10000 0 -0.32 1 1
EGFR -0.007 0.11 -10000 0 -0.52 11 11
EPHA2 0.011 0.05 -10000 0 -0.57 2 2
MYO6 0.032 0.054 -10000 0 -10000 0 0
CTNNB1 0.015 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.02 0.063 -10000 0 -0.34 8 8
AQP5 -0.012 0.044 -10000 0 -0.33 1 1
CTNND1 0.015 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.032 0.053 -10000 0 -0.25 9 9
regulation of calcium-dependent cell-cell adhesion 0.017 0.085 -10000 0 -0.49 2 2
EGF -0.014 0.11 -10000 0 -0.48 15 15
NCKAP1 0.015 0 -10000 0 -10000 0 0
AQP3 -0.094 0.19 -10000 0 -0.48 51 51
cortical microtubule organization -0.009 0.05 -10000 0 -0.28 9 9
GO:0000145 0.03 0.051 -10000 0 -0.24 9 9
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.025 0.057 -10000 0 -0.28 9 9
MLLT4 0.015 0 -10000 0 -10000 0 0
ARF6/GDP -0.012 0.051 -10000 0 -0.45 1 1
ARF6 0.015 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.029 0.053 -10000 0 -0.3 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.044 0.054 -10000 0 -10000 0 0
PVRL2 0.015 0 -10000 0 -10000 0 0
ZYX 0.031 0.057 -10000 0 -0.26 1 1
ARF6/GTP -0.008 0.041 -10000 0 -10000 0 0
CDH1 -0.004 0.1 -10000 0 -0.57 9 9
EGFR/EGFR/EGF/EGF -0.028 0.082 -10000 0 -0.49 3 3
RhoA/GDP -0.009 0.046 -10000 0 -10000 0 0
actin cytoskeleton organization 0.037 0.055 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.011 0.05 -10000 0 -0.56 2 2
GIT1 0.015 0 -10000 0 -10000 0 0
IGF1R 0.011 0.05 -10000 0 -0.57 2 2
IGF1 -0.25 0.29 -10000 0 -0.57 121 121
DIAPH1 -0.016 0.099 -10000 0 -0.58 8 8
Wnt receptor signaling pathway 0.009 0.05 0.28 9 -10000 0 9
RHOA 0.015 0 -10000 0 -10000 0 0
RhoA/GTP -0.013 0.051 -10000 0 -0.45 1 1
CTNNA1 0.015 0 -10000 0 -10000 0 0
VCL 0.038 0.056 -10000 0 -10000 0 0
EFNA1 0.002 0.08 -10000 0 -0.48 7 7
LPP 0.039 0.052 -10000 0 -10000 0 0
Ephrin A1/EPHA2 -0.015 0.061 -10000 0 -0.52 1 1
SEC6/SEC8 -0.007 0.039 -10000 0 -10000 0 0
MGAT3 0.017 0.086 -10000 0 -0.5 2 2
HGF/MET -0.068 0.11 -10000 0 -0.47 1 1
HGF -0.13 0.25 -10000 0 -0.56 66 66
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.026 0.05 -10000 0 -0.24 9 9
actin cable formation 0.075 0.053 -10000 0 -0.26 1 1
KIAA1543 0.032 0.087 -10000 0 -0.52 5 5
KIFC3 0.032 0.054 -10000 0 -0.26 9 9
NCK1 0.015 0 -10000 0 -10000 0 0
EXOC3 0.015 0 -10000 0 -10000 0 0
ACTN1 0.032 0.054 -10000 0 -10000 0 0
NCK1/GIT1 0.022 0 -10000 0 -10000 0 0
mol:GDP -0.009 0.05 -10000 0 -0.28 9 9
EXOC4 0.015 0 -10000 0 -10000 0 0
STX4 0.032 0.054 -10000 0 -0.26 9 9
PIP5K1C 0.032 0.054 -10000 0 -10000 0 0
LIMA1 0.015 0 -10000 0 -10000 0 0
ABI1 0.015 0 -10000 0 -10000 0 0
ROCK1 0.054 0.06 -10000 0 -0.39 1 1
adherens junction assembly 0.049 0.087 -10000 0 -0.5 5 5
IGF-1R heterotetramer/IGF1 -0.12 0.13 -10000 0 -0.52 3 3
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.022 0 -10000 0 -10000 0 0
MET 0.015 0 -10000 0 -10000 0 0
PLEKHA7 0.031 0.062 -10000 0 -0.55 1 1
mol:GTP 0.028 0.052 -10000 0 -0.3 2 2
establishment of epithelial cell apical/basal polarity 0.059 0.049 -10000 0 -10000 0 0
cortical actin cytoskeleton stabilization 0.026 0.05 -10000 0 -0.24 9 9
regulation of cell-cell adhesion 0.037 0.055 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.026 0.05 -10000 0 -0.24 9 9
Regulation of Telomerase

Figure S94.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S94.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Telomerase catalytic core complex -0.1 0.18 -9999 0 -0.56 6 6
RAD9A 0.006 0.068 -9999 0 -0.48 5 5
AP1 -0.12 0.21 -9999 0 -0.43 81 81
IFNAR2 0.01 0.009 -9999 0 -10000 0 0
AKT1 -0.027 0.09 -9999 0 -0.24 19 19
ER alpha/Oestrogen -0.067 0.16 -9999 0 -0.42 47 47
NFX1/SIN3/HDAC complex 0.033 0.028 -9999 0 -10000 0 0
EGF -0.016 0.12 -9999 0 -0.49 15 15
SMG5 0.015 0 -9999 0 -10000 0 0
SMG6 0.015 0 -9999 0 -10000 0 0
SP3/HDAC2 0.016 0.014 -9999 0 -10000 0 0
TERT/c-Abl -0.1 0.15 -9999 0 -0.52 6 6
SAP18 0.014 0.001 -9999 0 -10000 0 0
MRN complex 0.031 0 -9999 0 -10000 0 0
WT1 -0.061 0.17 -9999 0 -0.49 36 36
WRN 0.015 0 -9999 0 -10000 0 0
SP1 0.011 0.009 -9999 0 -10000 0 0
SP3 0.013 0.004 -9999 0 -10000 0 0
TERF2IP 0.015 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.1 0.12 -9999 0 -0.49 4 4
Mad/Max 0.014 0.026 -9999 0 -0.35 1 1
TERT -0.1 0.18 -9999 0 -0.57 6 6
CCND1 -0.1 0.21 -9999 0 -0.93 7 7
MAX 0.013 0.004 -9999 0 -10000 0 0
RBBP7 0.014 0.002 -9999 0 -10000 0 0
RBBP4 0.014 0.001 -9999 0 -10000 0 0
TERF2 0.014 0 -9999 0 -10000 0 0
PTGES3 0.015 0 -9999 0 -10000 0 0
SIN3A 0.014 0.001 -9999 0 -10000 0 0
Telomerase/911 0.026 0.037 -9999 0 -10000 0 0
CDKN1B -0.016 0.12 -9999 0 -10000 0 0
RAD1 0.015 0 -9999 0 -10000 0 0
XRCC5 0.015 0 -9999 0 -10000 0 0
XRCC6 0.015 0 -9999 0 -10000 0 0
SAP30 0.014 0.002 -9999 0 -10000 0 0
TRF2/PARP2 0 0 -9999 0 -10000 0 0
UBE3A 0.013 0.003 -9999 0 -10000 0 0
JUN -0.002 0.093 -9999 0 -0.57 7 7
E6 -0.002 0.004 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.008 0.007 -9999 0 -10000 0 0
FOS -0.16 0.27 -9999 0 -0.57 80 80
IFN-gamma/IRF1 -0.041 0.13 -9999 0 -0.32 48 48
PARP2 0.015 0 -9999 0 -10000 0 0
BLM 0 0.085 -9999 0 -0.48 8 8
Telomerase -0.004 0.057 -9999 0 -0.41 1 1
IRF1 0.018 0.005 -9999 0 -10000 0 0
ESR1 -0.088 0.22 -9999 0 -0.57 47 47
KU/TER 0.022 0 -9999 0 -10000 0 0
ATM/TRF2 0.024 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.04 0.028 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.037 0.03 -9999 0 -10000 0 0
HDAC1 0.014 0.001 -9999 0 -10000 0 0
HDAC2 0.011 0.009 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
SMAD3 0.028 0.004 -9999 0 -10000 0 0
ABL1 0.015 0 -9999 0 -10000 0 0
MXD1 0.011 0.031 -9999 0 -0.49 1 1
MRE11A 0.015 0 -9999 0 -10000 0 0
HUS1 0.015 0 -9999 0 -10000 0 0
RPS6KB1 0.015 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.11 0.15 -9999 0 -0.54 4 4
NR2F2 0.016 0.037 -9999 0 -0.57 1 1
MAPK3 0.012 0.01 -9999 0 -10000 0 0
MAPK1 0.012 0.01 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.016 0.002 -9999 0 -10000 0 0
NFKB1 0.015 0 -9999 0 -10000 0 0
HNRNPC 0.015 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0 0 -9999 0 -10000 0 0
NBN 0.015 0 -9999 0 -10000 0 0
EGFR -0.008 0.11 -9999 0 -0.52 11 11
mol:Oestrogen -0.001 0.002 -9999 0 -10000 0 0
EGF/EGFR -0.022 0.11 -9999 0 -0.35 26 26
MYC -0.018 0.12 -9999 0 -0.57 13 13
IL2 0 0.013 -9999 0 -10000 0 0
KU 0.022 0 -9999 0 -10000 0 0
RAD50 0.015 0 -9999 0 -10000 0 0
HSP90AA1 0.015 0 -9999 0 -10000 0 0
TGFB1 0.016 0.002 -9999 0 -10000 0 0
TRF2/BLM -0.009 0.053 -9999 0 -0.31 8 8
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.081 0.17 -9999 0 -0.53 5 5
SP1/HDAC2 0.018 0.015 -9999 0 -10000 0 0
PINX1 0.015 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.1 0.12 -9999 0 -0.49 4 4
Smad3/Myc 0.014 0.079 -9999 0 -0.34 13 13
911 complex 0.025 0.041 -9999 0 -0.27 5 5
IFNG -0.073 0.19 -9999 0 -0.48 48 48
Telomerase/PinX1 -0.1 0.12 -9999 0 -0.49 4 4
Telomerase/AKT1/mTOR/p70S6K -0.006 0.06 -9999 0 -10000 0 0
SIN3B 0.014 0.002 -9999 0 -10000 0 0
YWHAE 0.013 0.036 -9999 0 -0.57 1 1
Telomerase/EST1B -0.1 0.12 -9999 0 -0.52 3 3
response to DNA damage stimulus 0.004 0 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0 0 -9999 0 -10000 0 0
TRF2/WRN 0 0 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.1 0.12 -9999 0 -0.48 5 5
E2F1 -0.1 0.21 -9999 0 -0.49 62 62
ZNFX1 0.014 0.001 -9999 0 -10000 0 0
PIF1 -0.021 0.13 -9999 0 -0.49 19 19
NCL 0.015 0 -9999 0 -10000 0 0
DKC1 0.015 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Insulin Pathway

Figure S95.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S95.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.13 0.13 -9999 0 -0.53 3 3
TC10/GTP -0.12 0.12 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 0.025 0.051 -9999 0 -0.31 6 6
HRAS 0.015 0 -9999 0 -10000 0 0
APS homodimer 0.009 0.052 -9999 0 -0.48 3 3
GRB14 -0.047 0.16 -9999 0 -0.48 33 33
FOXO3 -0.025 0.11 -9999 0 -0.59 10 10
AKT1 0.023 0.083 -9999 0 -10000 0 0
INSR 0.017 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0.041 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.013 0.036 -9999 0 -0.57 1 1
SORBS1 -0.26 0.29 -9999 0 -0.57 125 125
CRK 0.015 0 -9999 0 -10000 0 0
PTPN1 0.039 0 -9999 0 -10000 0 0
CAV1 0.009 0.088 -9999 0 -0.33 16 16
CBL/APS/CAP/Crk-II/C3G -0.11 0.16 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/NCK2 0.025 0.051 -9999 0 -0.31 6 6
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.006 0.039 -9999 0 -0.26 6 6
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.038 0.036 -9999 0 -10000 0 0
RPS6KB1 0.03 0.078 -9999 0 -10000 0 0
PARD6A 0.013 0.036 -9999 0 -0.57 1 1
CBL 0.015 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0 0.009 -9999 0 -10000 0 0
PIK3R1 0.015 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.022 0.054 -9999 0 -10000 0 0
HRAS/GTP -0.01 0.046 -9999 0 -10000 0 0
Insulin Receptor 0.017 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.032 0.05 -9999 0 -0.28 6 6
PRKCI -0.007 0.031 -9999 0 -0.46 1 1
Insulin Receptor/Insulin/GRB14/PDK1 -0.028 0.069 -9999 0 -10000 0 0
SHC1 0.013 0.03 -9999 0 -0.48 1 1
negative regulation of MAPKKK cascade 0 0.007 -9999 0 -10000 0 0
PI3K -0.006 0.04 -9999 0 -0.27 6 6
NCK2 0.015 0 -9999 0 -10000 0 0
RHOQ 0.015 0 -9999 0 -10000 0 0
mol:H2O2 0 0 -9999 0 -10000 0 0
HRAS/GDP 0.011 0 -9999 0 -10000 0 0
AKT2 0.023 0.083 -9999 0 -10000 0 0
PRKCZ -0.009 0.043 -9999 0 -0.48 2 2
SH2B2 0.009 0.053 -9999 0 -0.48 3 3
SHC/SHIP 0.024 0.065 -9999 0 -0.27 12 12
F2RL2 -0.02 0.13 -9999 0 -0.53 17 17
TRIP10 0.013 0.036 -9999 0 -0.57 1 1
Insulin Receptor/Insulin/Shc 0.022 0.017 -9999 0 -0.26 1 1
TC10/GTP/CIP4/Exocyst 0.019 0.022 -9999 0 -0.35 1 1
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.039 0.016 -9999 0 -10000 0 0
RAPGEF1 0.015 0 -9999 0 -10000 0 0
RASA1 0.015 0 -9999 0 -10000 0 0
NCK1 0.015 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.12 0.17 -9999 0 -0.3 125 125
TC10/GDP 0.011 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.031 0.027 -9999 0 -0.28 2 2
INPP5D 0.016 0.066 -9999 0 -0.29 12 12
SOS1 0.015 0 -9999 0 -10000 0 0
SGK1 -0.035 0.17 -9999 0 -0.89 10 10
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.015 0 -9999 0 -10000 0 0
IRS1 0.002 0.086 -9999 0 -0.57 6 6
p62DOK/RasGAP 0 0.007 -9999 0 -10000 0 0
INS 0.003 0 -9999 0 -10000 0 0
mol:PI-3-4-P2 0.016 0.066 -9999 0 -0.29 12 12
GRB2 0.015 0 -9999 0 -10000 0 0
EIF4EBP1 0.02 0.091 -9999 0 -0.37 2 2
PTPRA 0.017 0 -9999 0 -10000 0 0
PIK3CA 0.015 0 -9999 0 -10000 0 0
TC10/GTP/CIP4 0.019 0.022 -9999 0 -0.35 1 1
PDPK1 0.015 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.031 0.042 -9999 0 -0.24 6 6
Insulin Receptor/Insulin/IRS1 0.015 0.051 -9999 0 -0.32 6 6
Insulin Receptor/Insulin/IRS3 0.015 0 -9999 0 -10000 0 0
Par3/Par6 0.015 0.076 -9999 0 -0.28 12 12
BARD1 signaling events

Figure S96.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S96.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.013 0.063 -10000 0 -0.41 6 6
ATM 0.015 0 -10000 0 -10000 0 0
UBE2D3 0.015 0 -10000 0 -10000 0 0
PRKDC 0.015 0 -10000 0 -10000 0 0
ATR 0.015 0 -10000 0 -10000 0 0
UBE2L3 0.015 0 -10000 0 -10000 0 0
FANCD2 0.028 0.016 -10000 0 -10000 0 0
protein ubiquitination -0.04 0.085 -10000 0 -10000 0 0
XRCC5 0.015 0 -10000 0 -10000 0 0
XRCC6 0.015 0 -10000 0 -10000 0 0
M/R/N Complex 0.031 0 -10000 0 -10000 0 0
MRE11A 0.015 0 -10000 0 -10000 0 0
DNA-PK 0.031 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.045 0.034 -10000 0 -10000 0 0
FANCF 0.011 0.047 -10000 0 -0.52 2 2
BRCA1 0.013 0.03 -10000 0 -0.48 1 1
CCNE1 -0.061 0.18 -10000 0 -0.48 41 41
CDK2/Cyclin E1 -0.033 0.13 -10000 0 -0.34 41 41
FANCG 0.015 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.011 0.067 -10000 0 -0.4 7 7
FANCE 0.015 0 -10000 0 -10000 0 0
FANCC 0.013 0.03 -10000 0 -0.48 1 1
NBN 0.015 0 -10000 0 -10000 0 0
FANCA -0.015 0.12 -10000 0 -0.48 16 16
DNA repair -0.015 0.12 -10000 0 -0.4 1 1
BRCA1/BARD1/ubiquitin 0.011 0.067 -10000 0 -0.4 7 7
BARD1/DNA-PK 0.031 0.05 -10000 0 -0.3 6 6
FANCL 0.013 0.03 -10000 0 -0.48 1 1
mRNA polyadenylation -0.013 0.063 0.4 6 -10000 0 6
BRCA1/BARD1/CTIP/M/R/N Complex 0.039 0.041 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1/TopBP1 0.021 0.057 -10000 0 -0.33 7 7
BRCA1/BARD1/P53 0.03 0.053 -10000 0 -0.29 7 7
BARD1/CSTF1/BRCA1 0.021 0.057 -10000 0 -0.33 7 7
BRCA1/BACH1 0.013 0.03 -10000 0 -0.48 1 1
BARD1 0.002 0.086 -10000 0 -0.57 6 6
PCNA 0.013 0.03 -10000 0 -0.48 1 1
BRCA1/BARD1/UbcH5C 0.021 0.057 -10000 0 -0.33 7 7
BRCA1/BARD1/UbcH7 0.021 0.057 -10000 0 -0.33 7 7
BRCA1/BARD1/RAD51/PCNA -0.062 0.14 -10000 0 -0.34 6 6
BARD1/DNA-PK/P53 0.038 0.047 -10000 0 -0.27 6 6
BRCA1/BARD1/Ubiquitin 0.011 0.067 -10000 0 -0.4 7 7
BRCA1/BARD1/CTIP 0.029 0.052 -10000 0 -0.3 6 6
FA complex 0.035 0.04 -10000 0 -10000 0 0
BARD1/EWS 0.013 0.063 -10000 0 -0.41 6 6
RBBP8 0.026 0 -10000 0 -10000 0 0
TP53 0.015 0 -10000 0 -10000 0 0
TOPBP1 0.015 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.029 0.052 0.29 7 -10000 0 7
BRCA1/BARD1 -0.003 0.1 -10000 0 -10000 0 0
CSTF1 0.015 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.001 0.063 -10000 0 -0.42 6 6
CDK2 0.015 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.15 0.23 -10000 0 -0.48 88 88
RAD50 0.015 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.011 0.067 -10000 0 -0.4 7 7
EWSR1 0.015 0 -10000 0 -10000 0 0
IFN-gamma pathway

Figure S97.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S97.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.003 0.087 -9999 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
CRKL 0.011 0.043 -9999 0 -0.48 2 2
STAT1 (dimer)/Cbp/p300 0.039 0.086 -9999 0 -0.34 3 3
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.005 0.022 -9999 0 -0.34 1 1
antigen processing and presentation of peptide antigen via MHC class I -0.031 0.064 -9999 0 -0.33 5 5
CaM/Ca2+ -0.03 0.062 -9999 0 -10000 0 0
RAP1A 0.015 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 0.01 0.091 -9999 0 -0.4 3 3
AKT1 0.025 0.075 -9999 0 -10000 0 0
MAP2K1 0.021 0.079 -9999 0 -10000 0 0
MAP3K11 0.011 0.082 -9999 0 -10000 0 0
IFNGR1 0.013 0.008 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.14 0.18 -9999 0 -0.4 86 86
Rap1/GTP -0.021 0.045 -9999 0 -10000 0 0
CRKL/C3G 0.02 0.031 -9999 0 -0.34 2 2
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0 0.095 -9999 0 -10000 0 0
CEBPB 0.055 0.084 -9999 0 -0.37 3 3
STAT3 0.015 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.009 0.089 -9999 0 -10000 0 0
STAT1 0.009 0.091 -9999 0 -0.4 3 3
CALM1 0.015 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.074 0.19 -9999 0 -0.47 48 48
PIK3CA 0.015 0 -9999 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.017 0.087 -9999 0 -0.37 3 3
CEBPB/PTGES2/Cbp/p300 -0.008 0.026 -9999 0 -10000 0 0
mol:Ca2+ 0.001 0.086 -9999 0 -10000 0 0
MAPK3 0.037 0.071 -9999 0 -10000 0 0
STAT1 (dimer) -0.04 0.088 -9999 0 -0.47 5 5
MAPK1 0.037 0.071 -9999 0 -10000 0 0
JAK2 0.011 0.036 -9999 0 -0.56 1 1
PIK3R1 0.015 0 -9999 0 -10000 0 0
JAK1 0.013 0.008 -9999 0 -10000 0 0
CAMK2D 0.015 0 -9999 0 -10000 0 0
DAPK1 0.052 0.092 -9999 0 -0.62 3 3
SMAD7 0.019 0.061 -9999 0 -0.35 1 1
CBL/CRKL/C3G 0.023 0.08 -9999 0 -0.36 1 1
PI3K -0.027 0.058 -9999 0 -10000 0 0
IFNG -0.074 0.19 -9999 0 -0.48 48 48
apoptosis 0.034 0.071 -9999 0 -0.44 3 3
CAMK2G 0.015 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.015 0 -9999 0 -10000 0 0
CAMK2A -0.17 0.27 -9999 0 -0.57 86 86
CAMK2B -0.038 0.15 -9999 0 -0.48 28 28
FRAP1 0.025 0.071 -9999 0 -10000 0 0
PRKCD 0.026 0.076 -9999 0 -10000 0 0
RAP1B 0.015 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.031 0.064 -9999 0 -0.33 5 5
PTPN2 0.015 0 -9999 0 -10000 0 0
EP300 0.016 0 -9999 0 -10000 0 0
IRF1 0.052 0.074 -9999 0 -10000 0 0
STAT1 (dimer)/PIASy 0.013 0.087 -9999 0 -0.38 3 3
SOCS1 0.005 0.021 -9999 0 -10000 0 0
mol:GDP -0.025 0.056 -9999 0 -0.35 1 1
CASP1 0.014 0.076 -9999 0 -0.29 9 9
PTGES2 0.015 0 -9999 0 -10000 0 0
IRF9 0.054 0.034 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.027 0.057 -9999 0 -10000 0 0
RAP1/GDP -0.021 0.045 -9999 0 -10000 0 0
CBL 0.01 0.082 -9999 0 -10000 0 0
MAP3K1 0.011 0.082 -9999 0 -10000 0 0
PIAS1 0.015 0 -9999 0 -10000 0 0
PIAS4 0.015 0 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.031 0.064 -9999 0 -0.33 5 5
PTPN11 0.001 0.085 -9999 0 -10000 0 0
CREBBP 0.016 0 -9999 0 -10000 0 0
RAPGEF1 0.015 0 -9999 0 -10000 0 0
EPHB forward signaling

Figure S98.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S98.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.007 0.091 -10000 0 -0.3 23 23
cell-cell adhesion 0.034 0.075 0.45 1 -10000 0 1
Ephrin B/EPHB2/RasGAP 0.016 0.085 -10000 0 -10000 0 0
ITSN1 0.015 0 -10000 0 -10000 0 0
PIK3CA 0.015 0 -10000 0 -10000 0 0
SHC1 0.013 0.03 -10000 0 -0.48 1 1
Ephrin B1/EPHB3 0.007 0.064 -10000 0 -0.29 12 12
Ephrin B1/EPHB1 -0.007 0.096 -10000 0 -0.34 20 20
HRAS/GDP -0.022 0.071 -10000 0 -0.48 1 1
Ephrin B/EPHB1/GRB7 -0.004 0.11 -10000 0 -0.57 1 1
Endophilin/SYNJ1 0.015 0.08 -10000 0 -10000 0 0
KRAS 0.013 0.03 -10000 0 -0.48 1 1
Ephrin B/EPHB1/Src 0.008 0.1 -10000 0 -0.28 26 26
endothelial cell migration 0 0 -10000 0 -10000 0 0
GRB2 0.015 0 -10000 0 -10000 0 0
GRB7 -0.008 0.11 -10000 0 -0.5 12 12
PAK1 0.018 0.088 -10000 0 -10000 0 0
HRAS 0.015 0 -10000 0 -10000 0 0
RRAS 0.014 0.082 -10000 0 -10000 0 0
DNM1 0.004 0.079 -10000 0 -0.57 5 5
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK 0.007 0.098 -10000 0 -0.54 1 1
lamellipodium assembly -0.034 0.075 -10000 0 -0.45 1 1
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.016 0.084 -10000 0 -0.24 19 19
PIK3R1 0.015 0 -10000 0 -10000 0 0
EPHB2 -0.015 0.12 -10000 0 -0.48 16 16
EPHB3 -0.008 0.1 -10000 0 -0.49 12 12
EPHB1 -0.028 0.15 -10000 0 -0.56 20 20
EPHB4 0.015 0 -10000 0 -10000 0 0
mol:GDP 0.021 0.087 -10000 0 -0.48 1 1
Ephrin B/EPHB2 0.007 0.085 -10000 0 -0.28 8 8
Ephrin B/EPHB3 0.011 0.084 -10000 0 -0.31 9 9
JNK cascade 0.004 0.1 -10000 0 -0.56 1 1
Ephrin B/EPHB1 -0.001 0.1 -10000 0 -0.29 26 26
RAP1/GDP 0.034 0.079 -10000 0 -0.41 1 1
EFNB2 0.015 0 -10000 0 -10000 0 0
EFNB3 -0.01 0.12 -10000 0 -0.54 12 12
EFNB1 0.015 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.012 0.11 -10000 0 -0.28 36 36
RAP1B 0.015 0 -10000 0 -10000 0 0
RAP1A 0.015 0 -10000 0 -10000 0 0
CDC42/GTP -0.033 0.077 -10000 0 -0.51 1 1
Rap1/GTP -0.033 0.074 -10000 0 -0.46 1 1
axon guidance -0.007 0.091 -10000 0 -0.3 23 23
MAPK3 0.031 0.076 -10000 0 -0.4 1 1
MAPK1 0.031 0.076 -10000 0 -0.4 1 1
Rac1/GDP 0.029 0.082 -10000 0 -0.44 1 1
actin cytoskeleton reorganization -0.024 0.055 -10000 0 -0.36 1 1
CDC42/GDP 0.029 0.082 -10000 0 -0.44 1 1
PI3K 0.036 0 -10000 0 -10000 0 0
EFNA5 0 0.093 -10000 0 -0.57 7 7
Ephrin B2/EPHB4 0.021 0 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.024 0.059 -10000 0 -10000 0 0
CDC42 0.015 0 -10000 0 -10000 0 0
RAS family/GTP -0.033 0.072 -10000 0 -0.44 1 1
PTK2 0.01 0.026 -10000 0 -10000 0 0
MAP4K4 0.004 0.1 -10000 0 -0.57 1 1
SRC 0.015 0 -10000 0 -10000 0 0
KALRN 0.007 0.066 -10000 0 -0.52 4 4
Intersectin/N-WASP 0.022 0 -10000 0 -10000 0 0
neuron projection morphogenesis 0.04 0.091 -10000 0 -0.34 3 3
MAP2K1 0.024 0.08 -10000 0 -0.42 1 1
WASL 0.015 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.003 0.11 -10000 0 -0.3 19 19
cell migration 0.028 0.091 -10000 0 -0.49 1 1
NRAS 0.015 0 -10000 0 -10000 0 0
SYNJ1 0.015 0.081 -10000 0 -10000 0 0
PXN 0.015 0 -10000 0 -10000 0 0
TF -0.012 0.12 -10000 0 -0.43 5 5
HRAS/GTP -0.037 0.082 -10000 0 -0.49 1 1
Ephrin B1/EPHB1-2 -0.012 0.11 -10000 0 -0.28 36 36
cell adhesion mediated by integrin 0.01 0.064 0.29 8 -10000 0 8
RAC1 0.015 0 -10000 0 -10000 0 0
mol:GTP 0 0.11 -10000 0 -0.52 1 1
RAC1-CDC42/GTP -0.041 0.085 -10000 0 -0.39 5 5
RASA1 0.015 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.034 0.079 -10000 0 -0.41 1 1
ruffle organization 0.024 0.099 -10000 0 -0.46 1 1
NCK1 0.015 0 -10000 0 -10000 0 0
receptor internalization 0.017 0.085 -10000 0 -10000 0 0
Ephrin B/EPHB2/KALRN 0.012 0.091 -10000 0 -10000 0 0
ROCK1 0.016 0.058 -10000 0 -0.25 12 12
RAS family/GDP -0.022 0.052 -10000 0 -0.35 1 1
Rac1/GTP -0.035 0.079 -10000 0 -0.48 1 1
Ephrin B/EPHB1/Src/Paxillin 0.012 0.088 -10000 0 -0.25 26 26
Signaling events mediated by PRL

Figure S99.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S99.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCNE1 -0.061 0.18 -9999 0 -0.48 41 41
mol:Halofuginone 0.006 0.001 -9999 0 -10000 0 0
ITGA1 0.015 0 -9999 0 -10000 0 0
CDKN1A 0.001 0.076 -9999 0 -0.67 1 1
PRL-3/alpha Tubulin 0.022 0 -9999 0 -10000 0 0
mol:Ca2+ -0.054 0.14 -9999 0 -0.42 34 34
AGT -0.059 0.19 -9999 0 -0.56 34 34
CCNA2 -0.094 0.17 -9999 0 -0.51 16 16
TUBA1B 0.015 0 -9999 0 -10000 0 0
EGR1 -0.072 0.18 -9999 0 -0.4 62 62
CDK2/Cyclin E1 -0.021 0.12 -9999 0 -0.38 10 10
MAPK3 0.026 0 -9999 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.022 0 -9999 0 -10000 0 0
MAPK1 0.026 0 -9999 0 -10000 0 0
PTP4A1 -0.035 0.14 -9999 0 -10000 0 0
PTP4A3 0.015 0 -9999 0 -10000 0 0
PTP4A2 0.015 0 -9999 0 -10000 0 0
ITGB1 0.026 0 -9999 0 -10000 0 0
SRC 0.015 0 -9999 0 -10000 0 0
RAC1 0.003 0.064 -9999 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0.022 0 -9999 0 -10000 0 0
PRL-1/ATF-5 -0.026 0.13 -9999 0 -10000 0 0
RABGGTA 0.015 0 -9999 0 -10000 0 0
BCAR1 0 0 -9999 0 -10000 0 0
RHOC 0.003 0.064 -9999 0 -10000 0 0
RHOA 0.003 0.064 -9999 0 -10000 0 0
cell motility 0.006 0.069 -9999 0 -10000 0 0
PRL-1/alpha Tubulin -0.025 0.13 -9999 0 -10000 0 0
PRL-3/alpha1 Integrin 0.022 0 -9999 0 -10000 0 0
ROCK1 0.006 0.069 -9999 0 -10000 0 0
RABGGTB 0.015 0 -9999 0 -10000 0 0
CDK2 0.015 0 -9999 0 -10000 0 0
mitosis -0.035 0.14 -9999 0 -10000 0 0
ATF5 0.013 0.03 -9999 0 -0.48 1 1
E-cadherin signaling events

Figure S100.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S100.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.017 0.075 -9999 0 -0.37 9 9
E-cadherin/beta catenin 0.008 0.077 -9999 0 -0.41 9 9
CTNNB1 0.015 0 -9999 0 -10000 0 0
JUP 0.013 0.036 -9999 0 -0.57 1 1
CDH1 -0.004 0.1 -9999 0 -0.57 9 9
EPO signaling pathway

Figure S101.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S101.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.056 0.094 -9999 0 -10000 0 0
CRKL 0.023 0.078 -9999 0 -0.28 3 3
mol:DAG 0.036 0.065 -9999 0 -10000 0 0
HRAS 0.051 0.067 -9999 0 -10000 0 0
MAPK8 0.007 0.092 -9999 0 -0.39 3 3
RAP1A 0.025 0.076 -9999 0 -0.28 3 3
GAB1 0.025 0.076 -9999 0 -0.28 3 3
MAPK14 0.011 0.083 -9999 0 -0.27 1 1
EPO -0.029 0.14 -9999 0 -0.48 24 24
PLCG1 0.036 0.066 -9999 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.004 0.079 -9999 0 -0.48 7 7
RAPGEF1 0.015 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.039 0.15 -9999 0 -0.39 31 31
GAB1/SHC/GRB2/SOS1 -0.017 0.045 -9999 0 -10000 0 0
EPO/EPOR (dimer) -0.015 0.11 -9999 0 -0.33 31 31
IRS2 0.015 0.094 -9999 0 -0.33 5 5
STAT1 0.04 0.083 -9999 0 -0.37 3 3
STAT5B 0.039 0.074 -9999 0 -0.32 3 3
cell proliferation 0.016 0.086 -9999 0 -0.4 2 2
GAB1/SHIP/PIK3R1/SHP2/SHC -0.02 0.056 -9999 0 -0.42 2 2
TEC 0.025 0.076 -9999 0 -0.28 1 1
SOCS3 -0.046 0.18 -9999 0 -0.57 28 28
STAT1 (dimer) 0.04 0.082 -9999 0 -0.36 3 3
JAK2 0.013 0.036 -9999 0 -0.56 1 1
PIK3R1 0.015 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.031 0.085 -9999 0 -0.3 3 3
EPO/EPOR -0.015 0.11 -9999 0 -0.33 31 31
LYN 0.017 0.004 -9999 0 -10000 0 0
TEC/VAV2 0.032 0.078 -9999 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0.004 0.079 -9999 0 -0.48 7 7
SHC1 0.013 0.03 -9999 0 -0.48 1 1
EPO/EPOR (dimer)/LYN 0.007 0.095 -9999 0 -0.31 3 3
mol:IP3 0.036 0.065 -9999 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.023 0.099 -9999 0 -0.41 4 4
SH2B3 0.016 0.006 -9999 0 -10000 0 0
NFKB1 0.011 0.083 -9999 0 -10000 0 0
EPO/EPOR (dimer)/JAK2/SOCS3 -0.037 0.083 -9999 0 -0.28 15 15
PTPN6 0.017 0.079 -9999 0 -0.3 3 3
TEC/VAV2/GRB2 0.038 0.075 -9999 0 -10000 0 0
EPOR 0.004 0.079 -9999 0 -0.48 7 7
INPP5D 0.002 0.086 -9999 0 -0.57 6 6
mol:GDP -0.017 0.046 -9999 0 -10000 0 0
SOS1 0.015 0 -9999 0 -10000 0 0
PLCG2 0.011 0.047 -9999 0 -0.52 2 2
CRKL/CBL/C3G 0.039 0.074 -9999 0 -10000 0 0
VAV2 0.023 0.079 -9999 0 -0.28 3 3
CBL 0.025 0.076 -9999 0 -0.28 3 3
SHC/Grb2/SOS1 -0.019 0.049 -9999 0 -10000 0 0
STAT5A 0.038 0.077 -9999 0 -0.32 3 3
GRB2 0.015 0 -9999 0 -10000 0 0
STAT5 (dimer) 0.052 0.099 -9999 0 -0.46 3 3
LYN/PLCgamma2 0.02 0.034 -9999 0 -0.37 2 2
PTPN11 0.015 0 -9999 0 -10000 0 0
BTK 0.009 0.1 -9999 0 -0.37 4 4
BCL2 0.031 0.2 -9999 0 -0.89 12 12
TRAIL signaling pathway

Figure S102.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S102.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 -0.009 0.11 -10000 0 -0.48 13 13
positive regulation of NF-kappaB transcription factor activity -0.001 0.092 -10000 0 -0.35 17 17
MAP2K4 0.045 0.03 -10000 0 -10000 0 0
IKBKB 0.015 0 -10000 0 -10000 0 0
TNFRSF10B 0.015 0 -10000 0 -10000 0 0
TNFRSF10A 0.013 0.036 -10000 0 -0.57 1 1
SMPD1 0.015 0.032 -10000 0 -10000 0 0
IKBKG 0.015 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.006 0.071 -10000 0 -0.57 4 4
TRAIL/TRAILR2 0.005 0.077 -10000 0 -0.34 13 13
TRAIL/TRAILR3 -0.004 0.096 -10000 0 -0.35 19 19
TRAIL/TRAILR1 0.003 0.081 -10000 0 -0.34 14 14
TRAIL/TRAILR4 -0.001 0.092 -10000 0 -0.35 17 17
TRAIL/TRAILR1/DAP3/GTP 0.015 0.063 -10000 0 -0.25 14 14
IKK complex -0.005 0.02 -10000 0 -10000 0 0
RIPK1 0.015 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.011 0 -10000 0 -10000 0 0
MAPK3 0.008 0.078 -10000 0 -0.34 13 13
MAP3K1 0.038 0.032 -10000 0 -10000 0 0
TRAILR4 (trimer) 0.006 0.07 -10000 0 -0.56 4 4
TRADD 0.015 0 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.013 0.035 -10000 0 -0.56 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.032 0.039 -10000 0 -10000 0 0
CFLAR 0.015 0 -10000 0 -10000 0 0
MAPK1 0.008 0.078 -10000 0 -0.34 13 13
TRAIL/TRAILR1/FADD/TRADD/RIP 0.026 0.068 -10000 0 -10000 0 0
mol:ceramide 0.015 0.032 -10000 0 -10000 0 0
FADD 0.006 0.068 -10000 0 -0.48 5 5
MAPK8 0.048 0.042 -10000 0 -10000 0 0
TRAF2 0.015 0 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.003 0.082 -10000 0 -0.54 6 6
CHUK 0.015 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.009 0.079 -10000 0 -0.28 19 19
DAP3 0.015 0 -10000 0 -10000 0 0
CASP10 -0.01 0.06 0.27 4 -10000 0 4
JNK cascade -0.001 0.092 -10000 0 -0.35 17 17
TRAIL (trimer) -0.009 0.11 -10000 0 -0.48 13 13
TNFRSF10C 0.003 0.082 -10000 0 -0.54 6 6
TRAIL/TRAILR1/DAP3/GTP/FADD 0.017 0.068 -10000 0 -0.28 1 1
TRAIL/TRAILR2/FADD 0.01 0.076 -10000 0 -0.27 18 18
cell death 0.015 0.032 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.033 0.035 -10000 0 -10000 0 0
TRAILR2 (trimer) 0.015 0 -10000 0 -10000 0 0
CASP8 0.004 0.02 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.028 0.065 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

Figure S103.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S103.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EEF2K 0.033 0 -9999 0 -10000 0 0
SNTA1 0.015 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.005 0.088 -9999 0 -0.28 24 24
MAPK12 0.026 0.048 -9999 0 -0.28 4 4
CCND1 0.013 0.058 -9999 0 -0.41 4 4
p38 gamma/SNTA1 0.032 0.045 -9999 0 -0.27 3 3
MAP2K3 0.015 0 -9999 0 -10000 0 0
PKN1 0.013 0.036 -9999 0 -0.57 1 1
G2/M transition checkpoint 0.026 0.048 -9999 0 -0.28 4 4
MAP2K6 0.021 0.046 -9999 0 -0.31 5 5
MAPT 0.005 0.095 -9999 0 -0.31 21 21
MAPK13 0.026 0 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.018 0.022 -9999 0 -0.34 1 1
HIV-1 Nef: Negative effector of Fas and TNF-alpha

Figure S104.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S104.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BAG4 0.015 0 -9999 0 -10000 0 0
Caspase 8 (4 units) -0.017 0.059 -9999 0 -0.36 2 2
NEF -0.009 0.05 -9999 0 -0.19 16 16
NFKBIA 0.012 0.026 -9999 0 -10000 0 0
BIRC3 0.014 0.15 -9999 0 -0.56 16 16
CYCS 0.03 0.082 -9999 0 -0.37 2 2
RIPK1 0.015 0 -9999 0 -10000 0 0
CD247 -0.006 0.095 -9999 0 -0.55 6 6
MAP2K7 0.038 0.063 -9999 0 -10000 0 0
protein ubiquitination 0.066 0.039 -9999 0 -10000 0 0
CRADD 0.015 0 -9999 0 -10000 0 0
DAXX 0.015 0 -9999 0 -10000 0 0
FAS 0.006 0.071 -9999 0 -0.57 4 4
BID 0.023 0.086 -9999 0 -0.39 2 2
NF-kappa-B/RelA/I kappa B alpha -0.016 0.063 -9999 0 -10000 0 0
TRADD 0.015 0 -9999 0 -10000 0 0
MAP3K5 0.015 0 -9999 0 -10000 0 0
CFLAR 0.015 0 -9999 0 -10000 0 0
FADD 0.006 0.068 -9999 0 -0.48 5 5
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.016 0.063 -9999 0 -10000 0 0
MAPK8 0.042 0.067 -9999 0 -10000 0 0
APAF1 0.015 0 -9999 0 -10000 0 0
TRAF1 0.015 0 -9999 0 -10000 0 0
TRAF2 0.015 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.016 0.088 -9999 0 -0.28 17 17
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.057 0.044 -9999 0 -10000 0 0
CHUK 0.068 0.04 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.035 0.052 -9999 0 -10000 0 0
TCRz/NEF -0.031 0.097 -9999 0 -0.31 27 27
TNF -0.009 0.11 -9999 0 -0.48 13 13
FASLG -0.026 0.18 -9999 0 -0.54 27 27
NFKB1 0.012 0.026 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.016 0.066 -9999 0 -0.27 13 13
CASP6 -0.009 0.036 -9999 0 -10000 0 0
CASP7 0.047 0.14 -9999 0 -0.5 14 14
RELA 0.012 0.026 -9999 0 -10000 0 0
CASP2 0.015 0 -9999 0 -10000 0 0
CASP3 0.047 0.14 -9999 0 -0.5 14 14
TNFRSF1A 0.015 0 -9999 0 -10000 0 0
TNFR1A/BAG4 0.022 0 -9999 0 -10000 0 0
CASP8 0.015 0 -9999 0 -10000 0 0
CASP9 0.015 0 -9999 0 -10000 0 0
MAP3K14 0.063 0.043 -9999 0 -10000 0 0
APAF-1/Caspase 9 -0.03 0.087 -9999 0 -0.36 14 14
BCL2 0.035 0.086 -9999 0 -0.39 1 1
Arf6 trafficking events

Figure S105.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S105.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.41 0.26 -10000 0 -0.57 195 195
CLTC 0.036 0.01 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.03 0.011 -10000 0 -10000 0 0
Dynamin 2/GTP 0.027 0.017 -10000 0 -0.25 1 1
EXOC4 0.015 0 -10000 0 -10000 0 0
CD59 0.032 0.008 -10000 0 -10000 0 0
CPE 0.01 0.061 -10000 0 -0.34 8 8
CTNNB1 0.015 0 -10000 0 -10000 0 0
membrane fusion 0.029 0.011 -10000 0 -10000 0 0
CTNND1 0.035 0.016 -10000 0 -10000 0 0
DNM2 0.015 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.036 0.007 -10000 0 -10000 0 0
TSHR 0.013 0.041 -10000 0 -0.28 5 5
INS 0.013 0.003 -10000 0 -10000 0 0
BIN1 -0.061 0.2 -10000 0 -0.57 35 35
mol:Choline 0.029 0.011 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.02 0.019 -10000 0 -0.28 1 1
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.015 0 -10000 0 -10000 0 0
mol:Ca2+ 0.026 0.017 -10000 0 -0.25 1 1
JUP 0.031 0.016 -10000 0 -10000 0 0
ASAP2/amphiphysin II -0.015 0.11 -10000 0 -0.31 35 35
ARF6/GTP 0.011 0 -10000 0 -10000 0 0
CDH1 0.024 0.042 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0.011 0 -10000 0 -10000 0 0
MAPK8IP3 0.007 0.063 -10000 0 -0.5 4 4
positive regulation of endocytosis 0.011 0 -10000 0 -10000 0 0
EXOC2 0.015 0 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.049 0 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.015 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.005 0.024 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.021 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.016 0.039 -10000 0 -0.3 4 4
ACAP1 0.023 0.028 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.059 0.11 -10000 0 -0.28 1 1
clathrin heavy chain/ACAP1 0.04 0.012 -10000 0 -10000 0 0
JIP4/KLC1 0.029 0 -10000 0 -10000 0 0
EXOC1 0.015 0 -10000 0 -10000 0 0
exocyst 0.049 0 -10000 0 -10000 0 0
RALA/GTP 0.011 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.021 0 -10000 0 -10000 0 0
receptor recycling 0.011 0 -10000 0 -10000 0 0
CTNNA1 0.035 0.016 -10000 0 -10000 0 0
NME1 0.02 0.019 -10000 0 -0.28 1 1
clathrin coat assembly 0.036 0.01 -10000 0 -10000 0 0
IL2RA 0.013 0.058 -10000 0 -10000 0 0
VAMP3 0.021 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.17 0.1 -10000 0 -0.28 10 10
EXOC6 0.015 0 -10000 0 -10000 0 0
PLD1 0.024 0.018 -10000 0 -0.28 1 1
PLD2 0.025 0 -10000 0 -10000 0 0
EXOC5 0.015 0 -10000 0 -10000 0 0
PIP5K1C 0.036 0.007 -10000 0 -10000 0 0
SDC1 0.029 0.025 -10000 0 -10000 0 0
ARF6/GDP 0.02 0.019 -10000 0 -0.28 1 1
EXOC7 0.015 0 -10000 0 -10000 0 0
E-cadherin/beta catenin -0.005 0.025 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.029 0.011 -10000 0 -10000 0 0
endocytosis 0.015 0.11 0.3 35 -10000 0 35
SCAMP2 0.015 0 -10000 0 -10000 0 0
ADRB2 0.018 0.082 -10000 0 -10000 0 0
EXOC3 0.015 0 -10000 0 -10000 0 0
ASAP2 0.015 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.028 0.017 -10000 0 -0.25 1 1
KLC1 0.015 0 -10000 0 -10000 0 0
AVPR2 0.012 0.089 -10000 0 -10000 0 0
RALA 0.015 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.004 0.021 -10000 0 -10000 0 0
PDGFR-beta signaling pathway

Figure S106.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S106.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.005 0.1 -9999 0 -0.53 5 5
PDGFB-D/PDGFRB/SLAP 0.005 0.095 -9999 0 -0.48 9 9
PDGFB-D/PDGFRB/APS/CBL 0.02 0.059 -9999 0 -0.31 8 8
AKT1 0.053 0.053 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.004 0.11 -9999 0 -0.58 5 5
PIK3CA 0.015 0 -9999 0 -10000 0 0
FGR -0.007 0.061 -9999 0 -0.39 6 6
mol:Ca2+ 0.018 0.089 -9999 0 -0.58 5 5
MYC 0.003 0.2 -9999 0 -0.75 16 16
SHC1 0.013 0.03 -9999 0 -0.48 1 1
HRAS/GDP 0.035 0.042 -9999 0 -10000 0 0
LRP1/PDGFRB/PDGFB 0.018 0.065 -9999 0 -0.33 9 9
GRB10 0.013 0.036 -9999 0 -0.57 1 1
PTPN11 0.015 0 -9999 0 -10000 0 0
GO:0007205 0.018 0.091 -9999 0 -0.6 5 5
PTEN 0.015 0 -9999 0 -10000 0 0
GRB2 0.015 0 -9999 0 -10000 0 0
GRB7 -0.008 0.11 -9999 0 -0.5 12 12
PDGFB-D/PDGFRB/SHP2 0.014 0.058 -9999 0 -0.41 5 5
PDGFB-D/PDGFRB/GRB10 0.012 0.064 -9999 0 -0.41 6 6
cell cycle arrest 0.005 0.095 -9999 0 -0.48 9 9
HRAS 0.015 0 -9999 0 -10000 0 0
HIF1A 0.058 0.05 -9999 0 -10000 0 0
GAB1 0.014 0.097 -9999 0 -0.57 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.018 0.092 -9999 0 -0.52 5 5
PDGFB-D/PDGFRB 0.021 0.053 -9999 0 -0.35 5 5
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.014 0.058 -9999 0 -0.41 5 5
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.028 0.085 -9999 0 -0.5 5 5
positive regulation of MAPKKK cascade 0.014 0.058 -9999 0 -0.4 5 5
PIK3R1 0.015 0 -9999 0 -10000 0 0
mol:IP3 0.018 0.091 -9999 0 -0.6 5 5
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.015 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.003 0.095 -9999 0 -0.37 17 17
SHB 0.015 0 -9999 0 -10000 0 0
BLK -0.056 0.16 -9999 0 -0.53 27 27
PTPN2 0.015 0.004 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.014 0.058 -9999 0 -0.41 5 5
BCAR1 0.015 0 -9999 0 -10000 0 0
VAV2 0.014 0.11 -9999 0 -0.48 8 8
CBL 0.015 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.013 0.07 -9999 0 -0.48 5 5
LCK -0.014 0.098 -9999 0 -0.52 8 8
PDGFRB 0.004 0.08 -9999 0 -0.57 5 5
ACP1 0.015 0 -9999 0 -10000 0 0
HCK -0.025 0.14 -9999 0 -0.62 12 12
ABL1 0.015 0.086 -9999 0 -0.51 5 5
PDGFB-D/PDGFRB/CBL 0.012 0.1 -9999 0 -0.64 5 5
PTPN1 0.015 0.004 -9999 0 -10000 0 0
SNX15 0.015 0 -9999 0 -10000 0 0
STAT3 0.015 0 -9999 0 -10000 0 0
STAT1 0.009 0.053 -9999 0 -0.48 3 3
cell proliferation 0.009 0.18 -9999 0 -0.66 16 16
SLA 0.002 0.086 -9999 0 -0.57 6 6
actin cytoskeleton reorganization 0.049 0.042 -9999 0 -10000 0 0
SRC -0.005 0.052 -9999 0 -0.36 5 5
PI3K -0.01 0.042 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC 0.008 0.083 -9999 0 -0.3 18 18
SH2B2 0.009 0.053 -9999 0 -0.48 3 3
PLCgamma1/SPHK1 0.004 0.11 -9999 0 -0.6 5 5
LYN -0.005 0.052 -9999 0 -0.36 5 5
LRP1 0.009 0.061 -9999 0 -0.57 3 3
SOS1 0.015 0 -9999 0 -10000 0 0
STAT5B 0.015 0 -9999 0 -10000 0 0
STAT5A 0.013 0.036 -9999 0 -0.57 1 1
NCK1-2/p130 Cas 0.001 0.039 -9999 0 -10000 0 0
SPHK1 -0.048 0.17 -9999 0 -0.48 34 34
EDG1 0 0.002 -9999 0 -10000 0 0
mol:DAG 0.018 0.091 -9999 0 -0.6 5 5
PLCG1 0.018 0.094 -9999 0 -0.62 5 5
NHERF/PDGFRB 0.013 0.073 -9999 0 -0.3 14 14
YES1 -0.005 0.052 -9999 0 -0.36 5 5
cell migration 0.01 0.073 -9999 0 -0.3 14 14
SHC/Grb2/SOS1 0 0.041 -9999 0 -10000 0 0
SLC9A3R2 0.015 0 -9999 0 -10000 0 0
SLC9A3R1 -0.002 0.09 -9999 0 -0.48 9 9
NHERF1-2/PDGFRB/PTEN 0.022 0.067 -9999 0 -0.3 5 5
FYN -0.011 0.073 -9999 0 -0.41 8 8
DOK1 0.028 0.049 -9999 0 -0.3 5 5
HRAS/GTP 0.011 0 -9999 0 -10000 0 0
PDGFB 0.013 0.03 -9999 0 -0.48 1 1
RAC1 0.017 0.13 -9999 0 -0.44 18 18
PRKCD 0.03 0.047 -9999 0 -0.3 5 5
FER 0.029 0.051 -9999 0 -0.3 6 6
MAPKKK cascade -0.005 0.036 -9999 0 -10000 0 0
RASA1 0.03 0.047 -9999 0 -0.3 5 5
NCK1 0.015 0 -9999 0 -10000 0 0
NCK2 0.015 0 -9999 0 -10000 0 0
p62DOK/Csk 0.037 0.045 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SHB 0.014 0.058 -9999 0 -0.41 5 5
chemotaxis 0.015 0.084 -9999 0 -0.49 5 5
STAT1-3-5/STAT1-3-5 -0.008 0.041 -9999 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0.002 0.058 -9999 0 -0.42 5 5
PTPRJ 0.013 0.036 -9999 0 -0.57 1 1
PLK2 and PLK4 events

Figure S107.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S107.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.015 0 -9999 0 -10000 0 0
PLK4 0.006 0.068 -9999 0 -0.48 5 5
regulation of centriole replication 0.019 0.049 -9999 0 -0.34 5 5
Retinoic acid receptors-mediated signaling

Figure S108.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S108.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.015 0 -10000 0 -10000 0 0
HDAC3 0.015 0 -10000 0 -10000 0 0
VDR 0.011 0.047 -10000 0 -0.52 2 2
Cbp/p300/PCAF 0.031 0 -10000 0 -10000 0 0
EP300 0.015 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.034 0.059 -10000 0 -0.25 2 2
KAT2B 0.015 0 -10000 0 -10000 0 0
MAPK14 0.015 0 -10000 0 -10000 0 0
AKT1 0.014 0.085 0.22 10 -0.26 19 29
RAR alpha/9cRA/Cyclin H -0.005 0.028 -10000 0 -0.27 1 1
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.028 0.068 -10000 0 -0.29 2 2
CDC2 0.001 0 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.018 0.055 -10000 0 -0.46 3 3
NCOR2 0.015 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.008 0.034 -10000 0 -0.38 2 2
RXRs/RARs/NRIP1/9cRA 0.013 0.092 -10000 0 -0.49 2 2
NCOA2 -0.02 0.14 -10000 0 -0.57 16 16
NCOA3 0.015 0 -10000 0 -10000 0 0
NCOA1 0.015 0 -10000 0 -10000 0 0
VDR/VDR/DNA 0.011 0.047 -10000 0 -0.52 2 2
RARG 0.016 0 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.021 0 -10000 0 -10000 0 0
MAPK3 0.016 0 -10000 0 -10000 0 0
MAPK1 0.015 0 -10000 0 -10000 0 0
MAPK8 0.01 0.061 -10000 0 -0.56 3 3
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.004 0.063 -10000 0 -0.38 2 2
RARA 0.024 0.038 -10000 0 -0.24 4 4
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.013 0.096 -10000 0 -0.43 4 4
PRKCA 0.017 0.036 -10000 0 -0.56 1 1
RXRs/RARs/NRIP1/9cRA/HDAC1 0.001 0.095 -10000 0 -0.54 2 2
RXRG -0.086 0.17 -10000 0 -0.34 79 79
RXRA 0.032 0.039 -10000 0 -0.24 2 2
RXRB 0.023 0.037 -10000 0 -0.34 1 1
VDR/Vit D3/DNA 0.008 0.034 -10000 0 -0.38 2 2
RBP1 -0.013 0.12 -10000 0 -0.56 13 13
CRBP1/9-cic-RA -0.009 0.091 -10000 0 -0.41 13 13
RARB -0.028 0.16 -10000 0 -0.57 21 21
PRKCG -0.002 0.079 -10000 0 -0.48 7 7
MNAT1 0.015 0 -10000 0 -10000 0 0
RAR alpha/RXRs 0.013 0.092 -10000 0 -0.43 2 2
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.018 0.085 -10000 0 -0.44 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.035 0.063 -10000 0 -0.34 2 2
RXRs/RARs/NRIP1/9cRA/HDAC3 0.001 0.095 -10000 0 -0.54 2 2
positive regulation of DNA binding -0.004 0.027 -10000 0 -0.26 1 1
NRIP1 0.003 0.089 -10000 0 -0.64 1 1
RXRs/RARs -0.007 0.096 -10000 0 -0.43 4 4
RXRs/RXRs/DNA/9cRA -0.016 0.055 -10000 0 -0.44 1 1
PRKACA 0.015 0 -10000 0 -10000 0 0
CDK7 0.015 0 -10000 0 -10000 0 0
TFIIH 0.031 0 -10000 0 -10000 0 0
RAR alpha/9cRA -0.003 0.017 -10000 0 -10000 0 0
CCNH 0.015 0 -10000 0 -10000 0 0
CREBBP 0.015 0 -10000 0 -10000 0 0
RAR gamma2/9cRA 0 0 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

Figure S109.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S109.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.011 0.043 -9999 0 -0.48 2 2
Rac1/GDP 0.002 0.01 -9999 0 -10000 0 0
DOCK1 0.013 0.036 -9999 0 -0.57 1 1
ITGA4 -0.006 0.11 -9999 0 -0.56 10 10
RAC1 0.015 0 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0 0.094 -9999 0 -0.4 14 14
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.015 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.017 0.069 -9999 0 -0.33 10 10
alpha4/beta7 Integrin/Paxillin 0.021 0.074 -9999 0 -0.3 13 13
lamellipodium assembly 0.001 0.02 -9999 0 -10000 0 0
PIK3CA 0.015 0 -9999 0 -10000 0 0
PI3K 0.022 0 -9999 0 -10000 0 0
ARF6 0.015 0 -9999 0 -10000 0 0
TLN1 0.015 0 -9999 0 -10000 0 0
PXN 0.026 0 -9999 0 -10000 0 0
PIK3R1 0.015 0 -9999 0 -10000 0 0
ARF6/GTP -0.009 0.045 -9999 0 -10000 0 0
cell adhesion 0.033 0.059 -9999 0 -0.27 9 9
CRKL/CBL 0.02 0.031 -9999 0 -0.34 2 2
alpha4/beta1 Integrin/Paxillin 0.026 0.063 -9999 0 -0.3 9 9
ITGB1 0.015 0 -9999 0 -10000 0 0
ITGB7 0.006 0.071 -9999 0 -0.57 4 4
ARF6/GDP 0.002 0.01 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.021 0.099 -9999 0 -0.35 16 16
p130Cas/Crk/Dock1 0.029 0.022 -9999 0 -0.34 1 1
VCAM1 -0.009 0.12 -9999 0 -0.57 11 11
alpha4/beta1 Integrin/Paxillin/Talin 0.034 0.059 -9999 0 -0.27 9 9
alpha4/beta1 Integrin/Paxillin/GIT1 0.034 0.059 -9999 0 -10000 0 0
BCAR1 0.015 0 -9999 0 -10000 0 0
mol:GDP -0.033 0.059 -9999 0 -10000 0 0
CBL 0.015 0 -9999 0 -10000 0 0
PRKACA 0.015 0 -9999 0 -10000 0 0
GIT1 0.015 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.034 0.059 -9999 0 -0.27 9 9
Rac1/GTP 0.001 0.022 -9999 0 -10000 0 0
TCGA08_rtk_signaling

Figure S110.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S110.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.072 0.21 -10000 0 -0.57 40 40
HRAS 0.015 0 -10000 0 -10000 0 0
EGFR -0.007 0.11 -10000 0 -0.52 11 11
AKT 0.028 0.064 -10000 0 -0.35 4 4
FOXO3 0.015 0 -10000 0 -10000 0 0
AKT1 0.015 0 -10000 0 -10000 0 0
FOXO1 0.015 0 -10000 0 -10000 0 0
AKT3 -0.007 0.11 -10000 0 -0.57 10 10
FOXO4 0.013 0.03 -10000 0 -0.48 1 1
MET 0.015 0 -10000 0 -10000 0 0
PIK3CA 0.015 0 -10000 0 -10000 0 0
PIK3CB 0.015 0 -10000 0 -10000 0 0
NRAS 0.015 0 -10000 0 -10000 0 0
PIK3CG -0.013 0.12 -10000 0 -0.55 13 13
PIK3R3 0.015 0 -10000 0 -10000 0 0
PIK3R2 0.015 0 -10000 0 -10000 0 0
NF1 0.015 0 -10000 0 -10000 0 0
RAS -0.002 0.068 -10000 0 -0.25 4 4
ERBB2 -0.002 0.09 -10000 0 -0.48 9 9
proliferation/survival/translation -0.033 0.031 0.19 1 -10000 0 1
PI3K 0.007 0.069 -10000 0 -0.21 8 8
PIK3R1 0.015 0 -10000 0 -10000 0 0
KRAS 0.013 0.03 -10000 0 -0.48 1 1
FOXO 0.045 0.028 -10000 0 -10000 0 0
AKT2 0.015 0 -10000 0 -10000 0 0
PTEN 0.015 0 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

Figure S111.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S111.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.03 0.091 -9999 0 -0.45 9 9
KLHL20 -0.012 0.038 -9999 0 -0.21 2 2
CYFIP2 -0.002 0.099 -9999 0 -0.57 8 8
Rac1/GDP 0.056 0.059 -9999 0 -10000 0 0
ENAH 0.031 0.09 -9999 0 -0.45 9 9
AP1M1 0.015 0 -9999 0 -10000 0 0
RAP1B 0.015 0 -9999 0 -10000 0 0
RAP1A 0.015 0 -9999 0 -10000 0 0
CTNNB1 0.015 0 -9999 0 -10000 0 0
CDC42/GTP -0.006 0.032 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.01 0.028 -9999 0 -0.14 2 2
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.023 0.077 -9999 0 -0.32 12 12
RAPGEF1 0.045 0.079 -9999 0 -0.38 9 9
CTNND1 0.015 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.021 0.092 -9999 0 -0.47 9 9
CRK 0.038 0.085 -9999 0 -0.42 9 9
E-cadherin/gamma catenin/alpha catenin 0.016 0.075 -9999 0 -0.37 9 9
alphaE/beta7 Integrin 0.016 0.052 -9999 0 -0.41 4 4
IQGAP1 0.015 0 -9999 0 -10000 0 0
NCKAP1 0.015 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.029 0.001 -9999 0 -10000 0 0
DLG1 0.031 0.09 -9999 0 -0.45 9 9
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.004 0.023 -9999 0 -10000 0 0
MLLT4 0.015 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.027 0.027 -9999 0 -0.28 2 2
PI3K -0.005 0.029 -9999 0 -10000 0 0
ARF6 0.015 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin 0.007 0.086 -9999 0 -0.44 9 9
TIAM1 0.013 0.036 -9999 0 -0.57 1 1
E-cadherin(dimer)/Ca2+ 0.024 0.057 -9999 0 -0.28 9 9
AKT1 -0.003 0.016 -9999 0 -10000 0 0
PIK3R1 0.015 0 -9999 0 -10000 0 0
CDH1 -0.004 0.1 -9999 0 -0.57 9 9
RhoA/GDP 0.056 0.059 -9999 0 -10000 0 0
actin cytoskeleton organization 0.039 0.044 -9999 0 -0.15 2 2
CDC42/GDP 0.056 0.059 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.018 0.058 -9999 0 -0.28 9 9
ITGB7 0.006 0.071 -9999 0 -0.57 4 4
RAC1 0.015 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.026 0.061 -9999 0 -0.3 9 9
E-cadherin/Ca2+/beta catenin/alpha catenin 0.015 0.057 -9999 0 -0.29 9 9
mol:GDP 0.052 0.066 -9999 0 -0.3 9 9
CDC42/GTP/IQGAP1 0.021 0 -9999 0 -10000 0 0
JUP 0.013 0.036 -9999 0 -0.57 1 1
p120 catenin/RhoA/GDP -0.009 0.046 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1 0.021 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0.022 0 -9999 0 -10000 0 0
RHOA 0.015 0 -9999 0 -10000 0 0
CDC42 0.015 0 -9999 0 -10000 0 0
CTNNA1 0.015 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.027 0.052 -9999 0 -0.19 12 12
NME1 0.013 0.03 -9999 0 -0.48 1 1
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.031 0.09 -9999 0 -0.45 9 9
regulation of cell-cell adhesion -0.005 0.028 -9999 0 -10000 0 0
WASF2 -0.005 0.014 -9999 0 -10000 0 0
Rap1/GTP -0.007 0.037 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.029 0.079 -9999 0 -0.57 2 2
CCND1 0.03 0.063 -9999 0 -0.23 12 12
VAV2 0.038 0.1 -9999 0 -0.45 11 11
RAP1/GDP 0.053 0.052 -9999 0 -10000 0 0
adherens junction assembly 0.031 0.087 -9999 0 -0.43 9 9
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.015 0 -9999 0 -10000 0 0
PIP5K1C 0.015 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.036 0.077 -9999 0 -0.54 2 2
E-cadherin/beta catenin -0.013 0.068 -9999 0 -0.38 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
SRC 0.029 0.09 -9999 0 -0.45 9 9
PIK3CA 0.015 0 -9999 0 -10000 0 0
Rac1/GTP -0.019 0.06 -9999 0 -0.34 2 2
E-cadherin/beta catenin/alpha catenin 0.017 0.066 -9999 0 -0.34 9 9
ITGAE 0.015 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.016 0.086 -9999 0 -0.48 9 9
Signaling events mediated by HDAC Class II

Figure S112.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S112.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G beta1gamma2/HDAC5 0.035 0.035 -10000 0 -0.3 3 3
HDAC3 0.015 0 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -10000 0 -10000 0 0
GATA1/HDAC4 0.019 0.005 -10000 0 -10000 0 0
GATA1/HDAC5 0.019 0.005 -10000 0 -10000 0 0
GATA2/HDAC5 0.005 0.081 -10000 0 -0.36 12 12
HDAC5/BCL6/BCoR 0.031 0 -10000 0 -10000 0 0
HDAC9 -0.022 0.14 -10000 0 -0.57 17 17
Glucocorticoid receptor/Hsp90/HDAC6 0.021 0.059 -10000 0 -0.34 7 7
HDAC4/ANKRA2 0.022 0 -10000 0 -10000 0 0
HDAC5/YWHAB 0.022 0 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.025 0 -10000 0 -10000 0 0
GATA2 -0.009 0.11 -10000 0 -0.52 12 12
HDAC4/RFXANK 0.021 0.022 -10000 0 -0.34 1 1
BCOR 0.015 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.015 0 -10000 0 -10000 0 0
HDAC5 0.015 0 -10000 0 -10000 0 0
GNB1/GNG2 0.018 0.045 -10000 0 -0.41 3 3
Histones 0.028 0.063 -10000 0 -0.23 2 2
ADRBK1 0.015 0 -10000 0 -10000 0 0
HDAC4 0.015 0 -10000 0 -10000 0 0
XPO1 0.015 0 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.022 0 -10000 0 -10000 0 0
HDAC4/Ubc9 0.022 0 -10000 0 -10000 0 0
HDAC7 0.015 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.021 0.026 -10000 0 -0.41 1 1
TUBA1B 0.015 0 -10000 0 -10000 0 0
HDAC6 0.015 0 -10000 0 -10000 0 0
HDAC5/RFXANK 0.021 0.022 -10000 0 -0.34 1 1
CAMK4 -0.007 0.11 -10000 0 -0.56 10 10
Tubulin/HDAC6 0.029 0.022 -10000 0 -0.34 1 1
SUMO1 0.015 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.015 0 -10000 0 -10000 0 0
GATA1 0.01 0.007 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.013 0.036 -10000 0 -0.57 1 1
NR3C1 0 0.093 -10000 0 -0.57 7 7
SUMO1/HDAC4 0.035 0 -10000 0 -10000 0 0
SRF 0.015 0 -10000 0 -10000 0 0
HDAC4/YWHAB 0.022 0 -10000 0 -10000 0 0
Tubulin 0.021 0.026 -10000 0 -0.41 1 1
HDAC4/14-3-3 E 0.021 0.026 -10000 0 -0.41 1 1
GNB1 0.015 0 -10000 0 -10000 0 0
RANGAP1 0.015 0 -10000 0 -10000 0 0
BCL6/BCoR 0.022 0 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.031 0 -10000 0 -10000 0 0
HDAC4/SRF 0.017 0.069 -10000 0 -0.33 10 10
HDAC4/ER alpha -0.053 0.16 -10000 0 -0.41 47 47
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.028 0.063 -10000 0 -0.23 2 2
cell motility 0.029 0.022 -10000 0 -0.34 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.015 0 -10000 0 -10000 0 0
HDAC7/HDAC3 0.022 0 -10000 0 -10000 0 0
BCL6 0.015 0 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.015 0 -10000 0 -10000 0 0
Hsp90/HDAC6 0.022 0 -10000 0 -10000 0 0
ESR1 -0.087 0.22 -10000 0 -0.57 47 47
HDAC6/HDAC11 0.018 0.043 -10000 0 -0.38 3 3
Ran/GTP/Exportin 1 0.038 0 -10000 0 -10000 0 0
NPC 0.009 0 -10000 0 -10000 0 0
MEF2C 0.002 0.086 -10000 0 -0.57 6 6
RAN 0.015 0 -10000 0 -10000 0 0
HDAC4/MEF2C 0.038 0.047 -10000 0 -10000 0 0
GNG2 0.009 0.061 -10000 0 -0.57 3 3
NCOR2 0.015 0 -10000 0 -10000 0 0
TUBB2A 0.013 0.036 -10000 0 -0.57 1 1
HDAC11 0.009 0.058 -10000 0 -0.54 3 3
HSP90AA1 0.015 0 -10000 0 -10000 0 0
RANBP2 0.015 0 -10000 0 -10000 0 0
ANKRA2 0.015 0 -10000 0 -10000 0 0
RFXANK 0.013 0.03 -10000 0 -0.48 1 1
nuclear import -0.032 0.021 0.31 1 -10000 0 1
Class I PI3K signaling events

Figure S113.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S113.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.001 0.01 -9999 0 -10000 0 0
DAPP1 0.013 0.093 -9999 0 -0.45 4 4
Src family/SYK family/BLNK-LAT/BTK-ITK 0.007 0.16 -9999 0 -0.48 17 17
mol:DAG 0.032 0.083 -9999 0 -0.22 12 12
HRAS 0.016 0.001 -9999 0 -10000 0 0
RAP1A 0.016 0.001 -9999 0 -10000 0 0
ARF5/GDP 0.039 0.046 -9999 0 -10000 0 0
PLCG2 0.011 0.047 -9999 0 -0.52 2 2
PLCG1 0.015 0 -9999 0 -10000 0 0
ARF5 0.015 0 -9999 0 -10000 0 0
mol:GTP -0.001 0.011 -9999 0 -10000 0 0
ARF1/GTP -0.001 0.009 -9999 0 -10000 0 0
RHOA 0.015 0 -9999 0 -10000 0 0
YES1 0.015 0 -9999 0 -10000 0 0
RAP1A/GTP -0.001 0.011 -9999 0 -10000 0 0
ADAP1 -0.004 0.032 -9999 0 -10000 0 0
ARAP3 -0.001 0.011 -9999 0 -10000 0 0
INPPL1 0.015 0 -9999 0 -10000 0 0
PREX1 0.015 0 -9999 0 -10000 0 0
ARHGEF6 0.011 0.05 -9999 0 -0.57 2 2
ARHGEF7 0.015 0 -9999 0 -10000 0 0
ARF1 0.015 0 -9999 0 -10000 0 0
NRAS 0.016 0.001 -9999 0 -10000 0 0
FYN 0.009 0.061 -9999 0 -0.57 3 3
ARF6 0.015 0 -9999 0 -10000 0 0
FGR 0.013 0.036 -9999 0 -0.57 1 1
mol:Ca2+ 0.028 0.048 -9999 0 -10000 0 0
mol:IP4 0 0 -9999 0 -10000 0 0
TIAM1 0.013 0.036 -9999 0 -0.57 1 1
ZAP70 -0.009 0.12 -9999 0 -0.57 11 11
mol:IP3 0.033 0.063 -9999 0 -0.2 2 2
LYN 0.015 0 -9999 0 -10000 0 0
ARF1/GDP 0.039 0.046 -9999 0 -10000 0 0
RhoA/GDP -0.002 0.011 -9999 0 -10000 0 0
PDK1/Src/Hsp90 0.031 0 -9999 0 -10000 0 0
BLNK -0.002 0.099 -9999 0 -0.57 8 8
actin cytoskeleton reorganization 0.062 0.043 -9999 0 -10000 0 0
SRC 0.015 0 -9999 0 -10000 0 0
PLEKHA2 0.025 0.055 -9999 0 -0.34 6 6
RAC1 0.015 0 -9999 0 -10000 0 0
PTEN 0 0.002 -9999 0 -10000 0 0
HSP90AA1 0.015 0 -9999 0 -10000 0 0
ARF6/GTP -0.001 0.01 -9999 0 -10000 0 0
RhoA/GTP -0.001 0.01 -9999 0 -10000 0 0
Src family/SYK family/BLNK-LAT 0.009 0.12 -9999 0 -0.43 11 11
BLK -0.056 0.18 -9999 0 -0.54 33 33
PDPK1 0.015 0 -9999 0 -10000 0 0
CYTH1 -0.001 0.01 -9999 0 -10000 0 0
HCK -0.01 0.12 -9999 0 -0.55 12 12
CYTH3 -0.001 0.01 -9999 0 -10000 0 0
CYTH2 -0.001 0.01 -9999 0 -10000 0 0
KRAS 0.014 0.03 -9999 0 -0.48 1 1
GO:0030676 0 0 -9999 0 -10000 0 0
FOXO3 0.031 0.094 -9999 0 -0.44 10 10
SGK1 -0.018 0.092 -9999 0 -0.48 10 10
INPP5D 0.002 0.086 -9999 0 -0.57 6 6
mol:GDP 0.032 0.048 -9999 0 -10000 0 0
SOS1 0.015 0 -9999 0 -10000 0 0
SYK 0.011 0.05 -9999 0 -0.57 2 2
ARF6/GDP -0.002 0.011 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.001 0.011 -9999 0 -10000 0 0
ARAP3/RAP1A/GTP -0.001 0.011 -9999 0 -10000 0 0
VAV1 -0.015 0.13 -9999 0 -0.56 14 14
mol:PI-3-4-P2 0.016 0.064 -9999 0 -0.41 6 6
RAS family/GTP/PI3K Class I 0.035 0.014 -9999 0 -10000 0 0
PLEKHA1 0.025 0.055 -9999 0 -0.34 6 6
Rac1/GDP 0.039 0.046 -9999 0 -10000 0 0
LAT 0.013 0.03 -9999 0 -0.48 1 1
Rac1/GTP 0.033 0.058 -9999 0 -0.27 3 3
ITK -0.027 0.078 -9999 0 -10000 0 0
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.033 0.11 -9999 0 -0.32 12 12
LCK 0.005 0.077 -9999 0 -0.55 5 5
BTK -0.014 0.056 -9999 0 -10000 0 0
E-cadherin signaling in keratinocytes

Figure S114.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S114.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
keratinocyte differentiation 0.05 0.038 -10000 0 -0.37 1 1
adherens junction organization 0.038 0.064 -10000 0 -0.28 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.046 0.063 -10000 0 -0.36 2 2
FMN1 0.03 0.073 -10000 0 -0.57 1 1
mol:IP3 0.041 0.038 -10000 0 -0.38 1 1
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.032 0.063 -10000 0 -0.29 9 9
CTNNB1 0.015 0.002 -10000 0 -10000 0 0
AKT1 0.047 0.043 -10000 0 -0.42 1 1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.033 0.085 -10000 0 -0.42 9 9
CTNND1 0.016 0.001 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.039 0.059 -10000 0 -0.56 1 1
VASP 0.039 0.06 -10000 0 -0.57 1 1
ZYX 0.038 0.063 -10000 0 -0.41 2 2
JUB 0.037 0.067 -10000 0 -0.52 2 2
EGFR(dimer) 0.028 0.083 -10000 0 -0.35 6 6
E-cadherin/beta catenin-gamma catenin -0.012 0.066 -10000 0 -0.35 9 9
mol:PI-3-4-5-P3 0.039 0.045 -10000 0 -0.44 1 1
PIK3CA 0.016 0.001 -10000 0 -10000 0 0
PI3K 0.04 0.046 -10000 0 -0.45 1 1
FYN 0.046 0.054 -10000 0 -0.29 4 4
mol:Ca2+ 0.041 0.037 -10000 0 -0.37 1 1
JUP 0.013 0.035 -10000 0 -0.56 1 1
PIK3R1 0.016 0.001 -10000 0 -10000 0 0
mol:DAG 0.041 0.038 -10000 0 -0.38 1 1
CDH1 -0.005 0.1 -10000 0 -0.56 9 9
RhoA/GDP 0.046 0.063 -10000 0 -0.36 2 2
establishment of polarity of embryonic epithelium 0.039 0.059 -10000 0 -0.56 1 1
SRC 0.015 0 -10000 0 -10000 0 0
RAC1 0.015 0 -10000 0 -10000 0 0
RHOA 0.015 0 -10000 0 -10000 0 0
EGFR -0.007 0.11 -10000 0 -0.52 11 11
CASR 0.04 0.047 -10000 0 -0.35 1 1
RhoA/GTP -0.004 0.026 -10000 0 -0.34 1 1
AKT2 0.047 0.043 -10000 0 -0.42 1 1
actin cable formation 0.037 0.071 -10000 0 -0.55 1 1
apoptosis -0.045 0.042 0.4 1 -10000 0 1
CTNNA1 0.016 0.001 -10000 0 -10000 0 0
mol:GDP 0.039 0.066 -10000 0 -0.39 2 2
PIP5K1A 0.039 0.06 -10000 0 -0.57 1 1
PLCG1 0.041 0.039 -10000 0 -0.39 1 1
Rac1/GTP -0.016 0.064 -10000 0 -0.49 2 2
homophilic cell adhesion 0.001 0.001 -10000 0 -10000 0 0
p38 MAPK signaling pathway

Figure S115.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S115.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.016 0 -9999 0 -10000 0 0
TRAF2/ASK1 0.021 0 -9999 0 -10000 0 0
ATM 0.015 0 -9999 0 -10000 0 0
MAP2K3 0.04 0.02 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.046 0.033 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
GADD45G 0.002 0.086 -9999 0 -0.57 6 6
TXN 0.009 0.011 -9999 0 -0.18 1 1
CALM1 0.015 0 -9999 0 -10000 0 0
GADD45A 0.015 0 -9999 0 -10000 0 0
GADD45B 0 0.093 -9999 0 -0.57 7 7
MAP3K1 0.015 0 -9999 0 -10000 0 0
MAP3K6 0.015 0 -9999 0 -10000 0 0
MAP3K7 0.015 0 -9999 0 -10000 0 0
MAP3K4 0.015 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
ASK1/ASK2 0.022 0 -9999 0 -10000 0 0
TAK1/TAB family 0 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3 0.028 0.017 -9999 0 -0.25 1 1
TRAF2 0.015 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0 0.01 -9999 0 -10000 0 0
TRAF6 0.01 0 -9999 0 -10000 0 0
RAC1 0.015 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
CAMK2B -0.038 0.15 -9999 0 -0.48 28 28
CCM2 0.013 0.03 -9999 0 -0.48 1 1
CaM/Ca2+/CAMKIIB -0.012 0.093 -9999 0 -0.28 28 28
MAPK11 0.015 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0 0.085 -9999 0 -0.25 28 28
OSM/MEKK3 0.021 0.022 -9999 0 -0.34 1 1
TAOK1 0.018 0.022 -9999 0 -0.34 1 1
TAOK2 0.02 0 -9999 0 -10000 0 0
TAOK3 0.02 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.015 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
MAP3K5 0.015 0 -9999 0 -10000 0 0
MAP3K10 0.013 0.03 -9999 0 -0.48 1 1
MAP3K3 0.015 0 -9999 0 -10000 0 0
TRX/ASK1 0.018 0.01 -9999 0 -10000 0 0
GADD45/MTK1/MTK1 0.021 0.073 -9999 0 -0.3 12 12
Canonical NF-kappaB pathway

Figure S116.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S116.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.019 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.089 0.025 -9999 0 -10000 0 0
ERC1 0.015 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.007 0.1 -9999 0 -0.34 22 22
NFKBIA 0.051 0 -9999 0 -10000 0 0
BIRC2 0.011 0.043 -9999 0 -0.48 2 2
IKBKB 0.015 0 -9999 0 -10000 0 0
RIPK2 0.015 0 -9999 0 -10000 0 0
IKBKG -0.005 0.019 -9999 0 -10000 0 0
IKK complex/A20 -0.012 0.045 -9999 0 -10000 0 0
NEMO/A20/RIP2 0.015 0 -9999 0 -10000 0 0
XPO1 0.015 0 -9999 0 -10000 0 0
NEMO/ATM 0.048 0.032 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.015 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0.021 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.003 0.011 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 0.031 0 -9999 0 -10000 0 0
NOD2 -0.026 0.14 -9999 0 -0.49 22 22
NFKB1 0.019 0 -9999 0 -10000 0 0
RELA 0.019 0 -9999 0 -10000 0 0
MALT1 0.015 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0.02 0.031 -9999 0 -0.34 2 2
ATM 0.015 0 -9999 0 -10000 0 0
TNF/TNFR1A 0.005 0.077 -9999 0 -0.34 13 13
TRAF6 0.015 0 -9999 0 -10000 0 0
PRKCA 0.013 0.036 -9999 0 -0.57 1 1
CHUK 0.015 0 -9999 0 -10000 0 0
UBE2D3 0.015 0 -9999 0 -10000 0 0
TNF -0.009 0.11 -9999 0 -0.48 13 13
NF kappa B1 p50/RelA 0 0 -9999 0 -10000 0 0
BCL10 0.015 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.051 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.019 0 -9999 0 -10000 0 0
TNFRSF1A 0.015 0 -9999 0 -10000 0 0
IKK complex 0.056 0.031 -9999 0 -10000 0 0
CYLD 0.015 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.004 0.017 -9999 0 -10000 0 0
Circadian rhythm pathway

Figure S117.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S117.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.051 0.035 -10000 0 -10000 0 0
CLOCK 0.019 0.002 -10000 0 -10000 0 0
TIMELESS/CRY2 0.048 0.025 -10000 0 -10000 0 0
DEC1/BMAL1 0.01 0.043 -10000 0 -0.33 4 4
ATR 0.015 0 -10000 0 -10000 0 0
NR1D1 0.047 0.015 -10000 0 -10000 0 0
ARNTL 0.019 0.002 -10000 0 -10000 0 0
TIMELESS 0.046 0.027 -10000 0 -10000 0 0
NPAS2 0.017 0.035 -10000 0 -0.56 1 1
CRY2 0.015 0 -10000 0 -10000 0 0
mol:CO -0.015 0.006 0.057 2 -10000 0 2
CHEK1 0.009 0.053 -10000 0 -0.48 3 3
mol:HEME 0.015 0.006 -10000 0 -0.057 2 2
PER1 -0.004 0.1 -10000 0 -0.57 9 9
BMAL/CLOCK/NPAS2 0.048 0.024 -10000 0 -0.32 1 1
BMAL1/CLOCK 0.052 0.034 -10000 0 -10000 0 0
S phase of mitotic cell cycle 0.051 0.035 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.052 0.035 -10000 0 -10000 0 0
mol:NADPH 0.015 0.006 -10000 0 -0.057 2 2
PER1/TIMELESS 0.037 0.065 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 -0.005 0.059 -10000 0 -0.48 4 4
Insulin-mediated glucose transport

Figure S118.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S118.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Insulin responsive Vesicles -0.13 0.082 -10000 0 -0.35 3 3
CaM/Ca2+ 0.011 0 -10000 0 -10000 0 0
AKT1 0.015 0 -10000 0 -10000 0 0
AKT2 0.015 0 -10000 0 -10000 0 0
STXBP4 0.015 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.13 0.11 0.21 1 -0.36 4 5
YWHAZ 0.015 0 -10000 0 -10000 0 0
CALM1 0.015 0 -10000 0 -10000 0 0
YWHAQ 0.015 0 -10000 0 -10000 0 0
TBC1D4 0.026 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.015 0 -10000 0 -10000 0 0
YWHAB 0.015 0 -10000 0 -10000 0 0
SNARE/Synip 0.031 0 -10000 0 -10000 0 0
YWHAG 0.015 0 -10000 0 -10000 0 0
ASIP 0.004 0.052 -10000 0 -0.48 3 3
PRKCI 0.015 0 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.011 0 -10000 0 -10000 0 0
RHOQ 0.015 0 -10000 0 -10000 0 0
GYS1 0.035 0 -10000 0 -10000 0 0
PRKCZ 0.013 0.036 -10000 0 -0.57 1 1
TRIP10 0.013 0.036 -10000 0 -0.57 1 1
TC10/GTP/CIP4/Exocyst 0.019 0.022 -10000 0 -0.35 1 1
AS160/14-3-3 0.04 0.042 -10000 0 -0.3 1 1
VAMP2 0.015 0 -10000 0 -10000 0 0
SLC2A4 -0.14 0.12 0.22 1 -0.4 4 5
STX4 0.015 0 -10000 0 -10000 0 0
GSK3B 0.029 0 -10000 0 -10000 0 0
SFN -0.036 0.15 -10000 0 -0.49 27 27
LNPEP 0.015 0 -10000 0 -10000 0 0
YWHAE 0.013 0.036 -10000 0 -0.57 1 1
mTOR signaling pathway

Figure S119.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S119.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.015 0 -10000 0 -10000 0 0
mol:PIP3 -0.006 0.042 -10000 0 -0.28 6 6
FRAP1 0.016 0.008 -10000 0 -10000 0 0
AKT1 0.026 0.038 -10000 0 -0.23 6 6
INSR 0.015 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.01 0 -10000 0 -10000 0 0
mol:GTP -0.004 0.025 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.001 0.006 -10000 0 -10000 0 0
TSC2 0.015 0 -10000 0 -10000 0 0
RHEB/GDP -0.003 0.02 -10000 0 -10000 0 0
TSC1 0.015 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.011 0.054 -10000 0 -0.35 6 6
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.001 0.007 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.015 0 -10000 0 -10000 0 0
RPS6KB1 0.029 0.02 -10000 0 -10000 0 0
MAP3K5 0.012 0 -10000 0 -10000 0 0
PIK3R1 0.015 0 -10000 0 -10000 0 0
apoptosis 0.012 0 -10000 0 -10000 0 0
mol:LY294002 0 0 -10000 0 -0.001 6 6
EIF4B 0.035 0.019 -10000 0 -10000 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.002 0.012 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1 0 0.001 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.021 0.05 -10000 0 -0.31 6 6
mTOR/RHEB/GTP/Raptor/GBL 0.033 0.013 -10000 0 -10000 0 0
FKBP1A 0.015 0 -10000 0 -10000 0 0
RHEB/GTP -0.003 0.02 -10000 0 -10000 0 0
mol:Amino Acids 0 0 -10000 0 -0.001 6 6
FKBP12/Rapamycin 0.012 0.002 -10000 0 -10000 0 0
PDPK1 -0.006 0.038 -10000 0 -0.25 6 6
EIF4E 0.015 0 -10000 0 -10000 0 0
ASK1/PP5C 0.025 0.006 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.019 0 -10000 0 -10000 0 0
TSC1/TSC2 0.04 0.033 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 0.001 6 -10000 0 6
RPS6 0.015 0 -10000 0 -10000 0 0
PPP5C 0.015 0 -10000 0 -10000 0 0
EIF4G1 0.015 0 -10000 0 -10000 0 0
IRS1 0.001 0.058 -10000 0 -0.38 6 6
INS 0 0 -10000 0 -10000 0 0
PTEN 0.015 0 -10000 0 -10000 0 0
PDK2 -0.006 0.038 -10000 0 -0.25 6 6
EIF4EBP1 0.012 0.01 -10000 0 -10000 0 0
PIK3CA 0.015 0 -10000 0 -10000 0 0
PPP2R5D 0.023 0.008 -10000 0 -10000 0 0
peptide biosynthetic process 0.02 0 -10000 0 -10000 0 0
RHEB 0.015 0 -10000 0 -10000 0 0
EIF4A1 0.015 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 -10000 0 -10000 0 0
EEF2 0.02 0 -10000 0 -10000 0 0
eIF4E/4E-BP1 0.02 0.009 -10000 0 -10000 0 0
ceramide signaling pathway

Figure S120.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S120.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.038 0.072 -10000 0 -10000 0 0
BAG4 0.015 0 -10000 0 -10000 0 0
BAD 0.031 0.024 -10000 0 -10000 0 0
NFKBIA 0.015 0 -10000 0 -10000 0 0
BIRC3 -0.019 0.14 -10000 0 -0.56 16 16
BAX 0.031 0.024 -10000 0 -10000 0 0
EnzymeConsortium:3.1.4.12 0.014 0.018 -10000 0 -10000 0 0
IKBKB 0.045 0.069 -10000 0 -10000 0 0
MAP2K2 0.044 0.025 -10000 0 -10000 0 0
MAP2K1 0.044 0.025 -10000 0 -10000 0 0
SMPD1 0.02 0.018 -10000 0 -10000 0 0
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.043 0.076 -10000 0 -10000 0 0
MAP2K4 0.039 0.023 -10000 0 -10000 0 0
protein ubiquitination 0.047 0.07 -10000 0 -10000 0 0
EnzymeConsortium:2.7.1.37 0.05 0.025 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.039 0.026 -10000 0 -10000 0 0
CRADD 0.015 0 -10000 0 -10000 0 0
mol:ceramide 0.024 0.025 -10000 0 -10000 0 0
I-kappa-B-alpha/RELA/p50/ubiquitin 0.021 0 -10000 0 -10000 0 0
MADD 0.015 0 -10000 0 -10000 0 0
MAP3K1 0.032 0.024 -10000 0 -10000 0 0
TRADD 0.015 0 -10000 0 -10000 0 0
RELA/p50 0.015 0 -10000 0 -10000 0 0
MAPK3 0.047 0.024 -10000 0 -10000 0 0
MAPK1 0.047 0.024 -10000 0 -10000 0 0
p50/RELA/I-kappa-B-alpha 0.022 0 -10000 0 -10000 0 0
FADD 0.035 0.079 -10000 0 -10000 0 0
KSR1 0.032 0.024 -10000 0 -10000 0 0
MAPK8 0.042 0.036 -10000 0 -0.22 3 3
TRAF2 0.015 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
CHUK 0.045 0.069 -10000 0 -10000 0 0
TNF R/SODD 0.022 0 -10000 0 -10000 0 0
TNF -0.009 0.11 -10000 0 -0.48 13 13
CYCS 0.037 0.031 0.14 10 -10000 0 10
IKBKG 0.045 0.069 -10000 0 -10000 0 0
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.032 0.074 -10000 0 -10000 0 0
RELA 0.015 0 -10000 0 -10000 0 0
RIPK1 0.015 0 -10000 0 -10000 0 0
AIFM1 0.037 0.031 0.14 10 -10000 0 10
TNF/TNF R/SODD 0.016 0.065 -10000 0 -0.27 13 13
TNFRSF1A 0.015 0 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.031 0.02 -10000 0 -10000 0 0
NSMAF 0.04 0.069 -10000 0 -10000 0 0
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
BCL2 -0.011 0.12 -10000 0 -0.57 12 12
HIF-2-alpha transcription factor network

Figure S121.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S121.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 0.007 0.023 -10000 0 -10000 0 0
oxygen homeostasis 0.01 0.016 -10000 0 -10000 0 0
TCEB2 0.013 0.03 -10000 0 -0.48 1 1
TCEB1 0.015 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0 0.038 -10000 0 -10000 0 0
EPO 0.12 0.2 -10000 0 -0.77 1 1
FIH (dimer) 0.026 0.015 -10000 0 -10000 0 0
APEX1 0.025 0.016 -10000 0 -10000 0 0
SERPINE1 0.14 0.2 -10000 0 -0.65 3 3
FLT1 0.01 0.02 -10000 0 -10000 0 0
ADORA2A 0.13 0.19 -10000 0 -0.66 1 1
germ cell development 0.1 0.24 -10000 0 -0.72 2 2
SLC11A2 0.14 0.19 -10000 0 -0.64 1 1
BHLHE40 0.14 0.2 -10000 0 -0.78 2 2
HIF1AN 0.026 0.015 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.078 0.13 -10000 0 -10000 0 0
ETS1 0.033 0 -10000 0 -10000 0 0
CITED2 0.007 0.017 -10000 0 -10000 0 0
KDR 0.01 0.02 -10000 0 -10000 0 0
PGK1 0.14 0.19 -10000 0 -0.64 1 1
SIRT1 0.015 0.002 -10000 0 -10000 0 0
response to hypoxia -0.001 0.004 -10000 0 -10000 0 0
HIF2A/ARNT 0.16 0.21 -10000 0 -0.65 2 2
EPAS1 0.089 0.098 -10000 0 -0.29 2 2
SP1 0.024 0.003 -10000 0 -10000 0 0
ABCG2 0.13 0.21 -10000 0 -0.65 2 2
EFNA1 0.14 0.2 -10000 0 -0.65 2 2
FXN 0.13 0.19 -10000 0 -0.66 1 1
POU5F1 0.1 0.24 -10000 0 -0.75 2 2
neuron apoptosis -0.16 0.21 0.63 2 -10000 0 2
EP300 0.015 0 -10000 0 -10000 0 0
EGLN3 0.013 0.088 -10000 0 -0.56 6 6
EGLN2 0.026 0.015 -10000 0 -10000 0 0
EGLN1 0.026 0.015 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.03 0.019 -10000 0 -0.27 1 1
VHL 0.015 0 -10000 0 -10000 0 0
ARNT 0.025 0.016 -10000 0 -10000 0 0
SLC2A1 0.13 0.19 -10000 0 -0.66 1 1
TWIST1 0.073 0.29 -10000 0 -0.62 21 21
ELK1 0.024 0 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.009 0.055 -10000 0 -10000 0 0
VEGFA 0.14 0.19 -10000 0 -0.64 1 1
CREBBP 0.015 0 -10000 0 -10000 0 0
FoxO family signaling

Figure S122.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S122.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.026 0.066 -9999 0 -10000 0 0
PLK1 -0.049 0.21 -9999 0 -0.59 2 2
CDKN1B 0.075 0.099 -9999 0 -10000 0 0
FOXO3 -0.011 0.17 -9999 0 -0.47 5 5
KAT2B 0.013 0.018 -9999 0 -10000 0 0
FOXO1/SIRT1 0.023 0.041 -9999 0 -10000 0 0
CAT -0.001 0.16 -9999 0 -10000 0 0
CTNNB1 0.015 0 -9999 0 -10000 0 0
AKT1 0.017 0.018 -9999 0 -10000 0 0
FOXO1 0.033 0.04 -9999 0 -10000 0 0
MAPK10 0.01 0.095 -9999 0 -0.28 25 25
mol:GTP 0.003 0 -9999 0 -10000 0 0
FOXO4 0.089 0.067 -9999 0 -10000 0 0
response to oxidative stress -0.001 0.022 -9999 0 -10000 0 0
FOXO3A/SIRT1 -0.052 0.11 -9999 0 -0.43 2 2
XPO1 0.016 0 -9999 0 -10000 0 0
EP300 0.016 0.004 -9999 0 -10000 0 0
BCL2L11 0.022 0.033 -9999 0 -10000 0 0
FOXO1/SKP2 0.032 0.05 -9999 0 -10000 0 0
mol:GDP -0.001 0.022 -9999 0 -10000 0 0
RAN 0.017 0 -9999 0 -10000 0 0
GADD45A 0.067 0.087 -9999 0 -10000 0 0
YWHAQ 0.015 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.074 0.034 -9999 0 -10000 0 0
MST1 -0.01 0.11 -9999 0 -0.49 12 12
CSNK1D 0.015 0 -9999 0 -10000 0 0
CSNK1E 0.015 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.054 0.045 -9999 0 -0.33 1 1
YWHAB 0.015 0 -9999 0 -10000 0 0
MAPK8 0.037 0.035 -9999 0 -0.28 3 3
MAPK9 0.04 0.009 -9999 0 -10000 0 0
YWHAG 0.015 0 -9999 0 -10000 0 0
YWHAE 0.013 0.036 -9999 0 -0.57 1 1
YWHAZ 0.015 0 -9999 0 -10000 0 0
SIRT1 0.013 0.017 -9999 0 -10000 0 0
SOD2 0.079 0.11 -9999 0 -10000 0 0
RBL2 0.033 0.13 -9999 0 -10000 0 0
RAL/GDP 0.025 0.018 -9999 0 -10000 0 0
CHUK 0.013 0.018 -9999 0 -10000 0 0
Ran/GTP 0.016 0 -9999 0 -10000 0 0
CSNK1G2 0.015 0 -9999 0 -10000 0 0
RAL/GTP 0.035 0.015 -9999 0 -10000 0 0
CSNK1G1 0.015 0 -9999 0 -10000 0 0
FASLG -0.068 0.35 -9999 0 -1.4 16 16
SKP2 0.006 0.068 -9999 0 -0.48 5 5
USP7 0.017 0 -9999 0 -10000 0 0
IKBKB 0.013 0.018 -9999 0 -10000 0 0
CCNB1 -0.048 0.21 -9999 0 -0.59 2 2
FOXO1-3a-4/beta catenin 0.096 0.11 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.032 0.05 -9999 0 -10000 0 0
CSNK1A1 0.015 0 -9999 0 -10000 0 0
SGK1 -0.009 0.11 -9999 0 -0.56 10 10
CSNK1G3 0.015 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.029 0.001 -9999 0 -10000 0 0
ZFAND5 0.092 0.06 -9999 0 -10000 0 0
SFN -0.036 0.15 -9999 0 -0.49 27 27
CDK2 0.015 0.008 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.042 0.061 -9999 0 -0.36 1 1
CREBBP 0.015 0.008 -9999 0 -10000 0 0
FBXO32 -0.001 0.16 -9999 0 -10000 0 0
BCL6 0.033 0.13 -9999 0 -10000 0 0
RALB 0.017 0 -9999 0 -10000 0 0
RALA 0.017 0 -9999 0 -10000 0 0
YWHAH 0.015 0 -9999 0 -10000 0 0
Atypical NF-kappaB pathway

Figure S123.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S123.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.021 0.026 -9999 0 -0.41 1 1
FBXW11 0.015 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.028 0.029 -9999 0 -0.3 2 2
NF kappa B1 p50/RelA/I kappa B alpha 0.049 0.032 -9999 0 -10000 0 0
NFKBIA 0.027 0.036 -9999 0 -0.21 6 6
MAPK14 0.015 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.03 0 -9999 0 -10000 0 0
ARRB2 0.02 0 -9999 0 -10000 0 0
REL 0.011 0.047 -9999 0 -0.52 2 2
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.029 0.022 -9999 0 -0.34 1 1
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.03 0 -9999 0 -10000 0 0
PIK3CA 0.015 0 -9999 0 -10000 0 0
NF kappa B1 p50 dimer 0.023 0 -9999 0 -10000 0 0
PIK3R1 0.015 0 -9999 0 -10000 0 0
NFKB1 0.026 0 -9999 0 -10000 0 0
RELA 0.015 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.035 0.036 -9999 0 -0.2 6 6
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.053 0.032 -9999 0 -10000 0 0
SRC 0.015 0 -9999 0 -10000 0 0
PI3K 0.022 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.035 0.037 -9999 0 -0.2 6 6
IKBKB 0.015 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.015 0 -9999 0 -10000 0 0
SYK 0.011 0.05 -9999 0 -0.57 2 2
I kappa B alpha/PIK3R1 0.034 0.034 -9999 0 -10000 0 0
cell death 0.051 0.031 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel 0.028 0.029 -9999 0 -0.3 2 2
LCK 0.005 0.077 -9999 0 -0.55 5 5
BCL3 0.013 0.036 -9999 0 -0.57 1 1
Signaling events mediated by VEGFR1 and VEGFR2

Figure S124.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S124.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaV beta3 Integrin -0.025 0.14 -9999 0 -0.42 29 29
AKT1 0.098 0.021 -9999 0 -10000 0 0
PTK2B 0.029 0.1 -9999 0 -0.45 2 2
VEGFR2 homodimer/Frs2 0.036 0.042 -9999 0 -10000 0 0
CAV1 -0.011 0.12 -9999 0 -0.57 12 12
CALM1 0.015 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.046 0.039 -9999 0 -10000 0 0
endothelial cell proliferation 0.056 0.093 -9999 0 -10000 0 0
mol:Ca2+ 0.063 0.019 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.059 0.01 -9999 0 -10000 0 0
RP11-342D11.1 0.053 0.018 -9999 0 -10000 0 0
CDH5 0.013 0.036 -9999 0 -0.57 1 1
VEGFA homodimer 0.04 0.017 -9999 0 -10000 0 0
SHC1 0.013 0.03 -9999 0 -0.48 1 1
SHC2 -0.019 0.14 -9999 0 -0.56 16 16
HRAS/GDP -0.001 0.015 -9999 0 -10000 0 0
SH2D2A 0.009 0.053 -9999 0 -0.48 3 3
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0 0.011 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.048 0.031 -9999 0 -10000 0 0
VEGFR1 homodimer 0.015 0 -9999 0 -10000 0 0
SHC/GRB2/SOS1 -0.001 0.016 -9999 0 -10000 0 0
GRB10 0.062 0.04 -9999 0 -0.59 1 1
PTPN11 0.015 0 -9999 0 -10000 0 0
GRB2 0.015 0 -9999 0 -10000 0 0
PAK1 0.013 0.036 -9999 0 -0.57 1 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.001 0.016 -9999 0 -10000 0 0
HRAS 0.015 0 -9999 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.032 0.078 -9999 0 -0.36 2 2
HIF1A 0.013 0.03 -9999 0 -0.48 1 1
FRS2 0.006 0.068 -9999 0 -0.48 5 5
oxygen and reactive oxygen species metabolic process 0 0.006 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.015 0 -9999 0 -10000 0 0
Nck/Pak 0.021 0.026 -9999 0 -0.41 1 1
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.048 0.037 -9999 0 -10000 0 0
mol:GDP -0.001 0.016 -9999 0 -10000 0 0
mol:NADP 0.087 0.016 -9999 0 -10000 0 0
eNOS/Hsp90 0.09 0.015 -9999 0 -10000 0 0
PIK3R1 0.015 0 -9999 0 -10000 0 0
mol:IP3 0.063 0.019 -9999 0 -10000 0 0
HIF1A/ARNT 0.021 0.022 -9999 0 -0.34 1 1
SHB 0.015 0 -9999 0 -10000 0 0
VEGFA 0.017 0.004 -9999 0 -10000 0 0
VEGFC 0.011 0.05 -9999 0 -0.57 2 2
FAK1/Vinculin 0.054 0.084 -9999 0 -0.39 1 1
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.015 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.023 0.1 -9999 0 -0.48 2 2
PTPN6 0.015 0 -9999 0 -10000 0 0
EPAS1 0.027 0.004 -9999 0 -10000 0 0
mol:L-citrulline 0.087 0.016 -9999 0 -10000 0 0
ITGAV 0.013 0.036 -9999 0 -0.57 1 1
PIK3CA 0.015 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.054 0.037 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer 0.057 0.02 -9999 0 -10000 0 0
VEGFR2/3 heterodimer 0.041 0.006 -9999 0 -10000 0 0
VEGFB 0.015 0 -9999 0 -10000 0 0
MAPK11 0.066 0.02 -9999 0 -10000 0 0
VEGFR2 homodimer 0.041 0.007 -9999 0 -10000 0 0
FLT1 0.015 0 -9999 0 -10000 0 0
NEDD4 0.017 0.004 -9999 0 -10000 0 0
MAPK3 0.032 0.063 -9999 0 -10000 0 0
MAPK1 0.032 0.063 -9999 0 -10000 0 0
VEGFA145/NRP2 0.005 0.089 -9999 0 -0.41 12 12
VEGFR1/2 heterodimer 0.041 0.006 -9999 0 -10000 0 0
KDR 0.041 0.007 -9999 0 -10000 0 0
VEGFA165/NRP1/VEGFR2 homodimer 0.049 0.07 -9999 0 -0.52 1 1
SRC 0.015 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process 0.037 0.059 -9999 0 -10000 0 0
PI3K 0.087 0.022 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.052 0.011 -9999 0 -10000 0 0
FES 0.062 0.027 -9999 0 -10000 0 0
GAB1 -0.001 0.01 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.052 0.011 -9999 0 -10000 0 0
CTNNB1 0.015 0 -9999 0 -10000 0 0
SOS1 0.015 0 -9999 0 -10000 0 0
ARNT 0.015 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.078 0.056 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Yes 0.052 0.011 -9999 0 -10000 0 0
PI3K/GAB1 0.1 0.021 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.005 0.029 -9999 0 -10000 0 0
PRKACA 0.015 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.045 0.029 -9999 0 -10000 0 0
HSP90AA1 0.015 0 -9999 0 -10000 0 0
CDC42 0.063 0.019 -9999 0 -10000 0 0
actin cytoskeleton reorganization 0.048 0.031 -9999 0 -10000 0 0
PTK2 0.048 0.087 -9999 0 -0.42 1 1
EDG1 0.053 0.018 -9999 0 -10000 0 0
mol:DAG 0.063 0.019 -9999 0 -10000 0 0
CaM/Ca2+ 0.065 0.017 -9999 0 -10000 0 0
MAP2K3 0.068 0.028 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.063 0.04 -9999 0 -0.6 1 1
PLCG1 0.063 0.019 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.059 0.01 -9999 0 -10000 0 0
IQGAP1 0.015 0 -9999 0 -10000 0 0
YES1 0.015 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.052 0.011 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.052 0.011 -9999 0 -10000 0 0
cell migration 0.078 0.078 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0.085 0.021 -9999 0 -10000 0 0
FYN 0.009 0.061 -9999 0 -0.57 3 3
VEGFB/NRP1 0.059 0.018 -9999 0 -10000 0 0
mol:NO 0.087 0.016 -9999 0 -10000 0 0
PXN 0.015 0 -9999 0 -10000 0 0
HRAS/GTP -0.001 0.015 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.063 0.04 -9999 0 -0.59 1 1
VHL 0.015 0 -9999 0 -10000 0 0
ITGB3 -0.048 0.18 -9999 0 -0.57 29 29
NOS3 0.09 0.017 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Sck 0.032 0.079 -9999 0 -10000 0 0
RAC1 0.015 0 -9999 0 -10000 0 0
PRKCA 0.068 0.026 -9999 0 -10000 0 0
PRKCB -0.017 0.14 -9999 0 -0.51 1 1
VCL 0.013 0.036 -9999 0 -0.57 1 1
VEGFA165/NRP1 0.054 0.018 -9999 0 -10000 0 0
VEGFR1/2 heterodimer/VEGFA homodimer 0.052 0.011 -9999 0 -10000 0 0
VEGFA165/NRP2 0.005 0.089 -9999 0 -0.41 12 12
MAPKKK cascade 0.084 0.037 -9999 0 -0.48 1 1
NRP2 -0.011 0.12 -9999 0 -0.57 12 12
VEGFC homodimer 0.011 0.05 -9999 0 -0.56 2 2
NCK1 0.015 0 -9999 0 -10000 0 0
ROCK1 0.015 0 -9999 0 -10000 0 0
FAK1/Paxillin 0.055 0.083 -9999 0 -0.39 1 1
MAP3K13 0.061 0.029 -9999 0 -10000 0 0
PDPK1 0.089 0.02 -9999 0 -10000 0 0
VEGFR1 specific signals

Figure S125.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S125.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR1 homodimer/VEGFB homodimer 0.036 0.018 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP1 0.025 0.018 -9999 0 -0.27 1 1
mol:DAG 0.036 0.047 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 0.033 0.016 -9999 0 -10000 0 0
CaM/Ca2+ 0.043 0.044 -9999 0 -10000 0 0
HIF1A 0.022 0.03 -9999 0 -0.47 1 1
GAB1 0.015 0 -9999 0 -10000 0 0
AKT1 0.06 0.036 -9999 0 -10000 0 0
PLCG1 0.037 0.047 -9999 0 -10000 0 0
NOS3 0.065 0.036 -9999 0 -10000 0 0
CBL 0.015 0 -9999 0 -10000 0 0
mol:NO 0.064 0.035 -9999 0 -10000 0 0
FLT1 0.034 0.022 -9999 0 -0.32 1 1
PGF 0.002 0.08 -9999 0 -0.48 7 7
VEGFR1 homodimer/NRP2/VEGFR121 0.028 0.071 -9999 0 -10000 0 0
CALM1 0.015 0 -9999 0 -10000 0 0
PIK3CA 0.015 0 -9999 0 -10000 0 0
eNOS/Hsp90 0.071 0.034 -9999 0 -10000 0 0
endothelial cell proliferation -0.017 0.12 -9999 0 -0.4 3 3
mol:Ca2+ 0.036 0.047 -9999 0 -10000 0 0
MAPK3 0.048 0.045 -9999 0 -10000 0 0
MAPK1 0.048 0.045 -9999 0 -10000 0 0
PIK3R1 0.015 0 -9999 0 -10000 0 0
PLGF homodimer 0.002 0.079 -9999 0 -0.48 7 7
PRKACA 0.015 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.011 0.12 -9999 0 -0.57 12 12
VEGFA homodimer 0.015 0 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.036 0.018 -9999 0 -10000 0 0
platelet activating factor biosynthetic process 0.055 0.044 -9999 0 -10000 0 0
PI3K 0.044 0.044 -9999 0 -10000 0 0
PRKCA 0.042 0.047 -9999 0 -10000 0 0
PRKCB -0.046 0.15 -9999 0 -0.51 2 2
VEGFR1 homodimer/PLGF homodimer 0.028 0.052 -9999 0 -10000 0 0
VEGFA 0.015 0 -9999 0 -10000 0 0
VEGFB 0.015 0 -9999 0 -10000 0 0
mol:IP3 0.036 0.047 -9999 0 -10000 0 0
RASA1 0.044 0.016 -9999 0 -10000 0 0
NRP2 -0.011 0.12 -9999 0 -0.57 12 12
VEGFR1 homodimer 0.034 0.022 -9999 0 -0.32 1 1
VEGFB homodimer 0.015 0 -9999 0 -10000 0 0
NCK1 0.015 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.058 0.07 -9999 0 -0.39 1 1
PTPN11 0.015 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0.042 0.044 -9999 0 -10000 0 0
mol:L-citrulline 0.064 0.035 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.051 0.016 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.043 0.016 -9999 0 -10000 0 0
CD2AP 0.015 0 -9999 0 -10000 0 0
PI3K/GAB1 0.049 0.042 -9999 0 -10000 0 0
PDPK1 0.049 0.042 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.043 0.016 -9999 0 -10000 0 0
mol:NADP 0.064 0.035 -9999 0 -10000 0 0
HSP90AA1 0.015 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.049 0.015 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.02 0.078 -9999 0 -0.33 12 12
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

Figure S126.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S126.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.015 0 -9999 0 -10000 0 0
SMAD2 0.016 0 -9999 0 -10000 0 0
SMAD3 0.047 0 -9999 0 -10000 0 0
SMAD3/SMAD4 0.053 0.005 -9999 0 -10000 0 0
SMAD4/Ubc9/PIASy 0.031 0 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.043 0.021 -9999 0 -10000 0 0
PPM1A 0.015 0 -9999 0 -10000 0 0
CALM1 0.015 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0.024 0 -9999 0 -10000 0 0
MAP3K1 0.015 0 -9999 0 -10000 0 0
TRAP-1/SMAD4 0.016 0.052 -9999 0 -0.41 4 4
MAPK3 0.015 0 -9999 0 -10000 0 0
MAPK1 0.015 0 -9999 0 -10000 0 0
NUP214 0.015 0 -9999 0 -10000 0 0
CTDSP1 0.015 0 -9999 0 -10000 0 0
CTDSP2 0.015 0 -9999 0 -10000 0 0
CTDSPL 0.015 0 -9999 0 -10000 0 0
KPNB1 0.015 0 -9999 0 -10000 0 0
TGFBRAP1 0.006 0.071 -9999 0 -0.57 4 4
UBE2I 0.015 0 -9999 0 -10000 0 0
NUP153 0.015 0 -9999 0 -10000 0 0
KPNA2 0.011 0.043 -9999 0 -0.48 2 2
PIAS4 0.015 0 -9999 0 -10000 0 0
Arf6 downstream pathway

Figure S127.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S127.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.049 0.004 -10000 0 -10000 0 0
regulation of axonogenesis -0.032 0.016 -10000 0 -10000 0 0
myoblast fusion -0.022 0.013 -10000 0 -10000 0 0
mol:GTP 0 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.038 0.029 0.28 2 -10000 0 2
ARF1/GTP 0 0.001 -10000 0 -10000 0 0
mol:GM1 0.012 0.004 -10000 0 -10000 0 0
mol:Choline 0.031 0.023 -10000 0 -0.34 1 1
lamellipodium assembly -0.001 0.014 -10000 0 -10000 0 0
MAPK3 0.034 0.003 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.039 0.029 -10000 0 -0.28 2 2
ARF1 0.015 0 -10000 0 -10000 0 0
ARF6/GDP 0.022 0.014 -10000 0 -10000 0 0
ARF1/GDP 0.03 0.013 -10000 0 -10000 0 0
ARF6 0.014 0.002 -10000 0 -10000 0 0
RAB11A 0.015 0 -10000 0 -10000 0 0
TIAM1 0.015 0.036 -10000 0 -0.56 1 1
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.034 0.003 -10000 0 -10000 0 0
actin filament bundle formation -0.029 0.012 -10000 0 -10000 0 0
KALRN -0.003 0.033 -10000 0 -0.26 4 4
RAB11FIP3/RAB11A 0.022 0 -10000 0 -10000 0 0
RhoA/GDP 0.03 0.012 -10000 0 -10000 0 0
NME1 0.015 0.03 -10000 0 -0.48 1 1
Rac1/GDP 0.03 0.012 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0 0.003 -10000 0 -10000 0 0
cortical actin cytoskeleton organization -0.001 0.014 -10000 0 -10000 0 0
RAC1 0.015 0 -10000 0 -10000 0 0
liver development 0 0.003 -10000 0 -10000 0 0
ARF6/GTP 0 0.003 -10000 0 -10000 0 0
RhoA/GTP 0 0.001 -10000 0 -10000 0 0
mol:GDP -0.001 0.013 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A 0 0.002 -10000 0 -10000 0 0
RHOA 0.015 0 -10000 0 -10000 0 0
PLD1 0.023 0.026 -10000 0 -0.4 1 1
RAB11FIP3 0.015 0 -10000 0 -10000 0 0
tube morphogenesis -0.001 0.014 -10000 0 -10000 0 0
ruffle organization 0.032 0.016 -10000 0 -10000 0 0
regulation of epithelial cell migration 0 0.003 -10000 0 -10000 0 0
PLD2 0.024 0.004 -10000 0 -10000 0 0
PIP5K1A 0.032 0.016 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.031 0.023 -10000 0 -0.34 1 1
Rac1/GTP -0.001 0.014 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

Figure S128.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S128.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NF kappa B/RelA -0.008 0.034 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.047 0.032 -9999 0 -10000 0 0
SUMO1 0.015 0 -9999 0 -10000 0 0
ZFPM1 0.015 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.025 0 -9999 0 -10000 0 0
FKBP3 0.015 0 -9999 0 -10000 0 0
Histones 0.046 0.026 -9999 0 -10000 0 0
YY1/LSF 0.035 0 -9999 0 -10000 0 0
SMG5 0.015 0 -9999 0 -10000 0 0
RAN 0.015 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 0.031 0.036 -9999 0 -10000 0 0
I kappa B alpha/HDAC1 0.031 0.028 -9999 0 -10000 0 0
SAP18 0.015 0 -9999 0 -10000 0 0
RELA 0.037 0.03 -9999 0 -10000 0 0
HDAC1/Smad7 0.029 0.022 -9999 0 -0.34 1 1
RANGAP1 0.015 0 -9999 0 -10000 0 0
HDAC3/TR2 0.031 0.028 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.054 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.04 0.027 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 -0.009 0.11 -9999 0 -0.52 12 12
GATA1 0.01 0.007 -9999 0 -10000 0 0
Mad/Max 0.021 0.022 -9999 0 -0.34 1 1
NuRD/MBD3 Complex/GATA1/Fog1 0.064 0.003 -9999 0 -10000 0 0
RBBP7 0.015 0 -9999 0 -10000 0 0
NPC 0.009 0 -9999 0 -10000 0 0
RBBP4 0.015 0 -9999 0 -10000 0 0
MAX 0.015 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.015 0 -9999 0 -10000 0 0
NFKBIA 0.025 0.032 -9999 0 -10000 0 0
KAT2B 0.015 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.049 0 -9999 0 -10000 0 0
SIN3 complex 0.039 0 -9999 0 -10000 0 0
SMURF1 0.015 0 -9999 0 -10000 0 0
CHD3 0.015 0 -9999 0 -10000 0 0
SAP30 0.015 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.015 0 -9999 0 -10000 0 0
YY1/HDAC3 0.044 0.026 -9999 0 -10000 0 0
YY1/HDAC2 0.035 0 -9999 0 -10000 0 0
YY1/HDAC1 0.035 0 -9999 0 -10000 0 0
NuRD/MBD2 Complex (MeCP1) 0.054 0 -9999 0 -10000 0 0
PPARG 0.01 0.1 -9999 0 -0.32 21 21
HDAC8/hEST1B 0.031 0 -9999 0 -10000 0 0
UBE2I 0.015 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.015 0 -9999 0 -10000 0 0
TNFRSF1A 0.015 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.031 0.028 -9999 0 -10000 0 0
MBD3L2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.029 0.022 -9999 0 -0.34 1 1
CREBBP 0.015 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.058 0 -9999 0 -10000 0 0
HDAC1 0.015 0 -9999 0 -10000 0 0
HDAC3 0.025 0.032 -9999 0 -10000 0 0
HDAC2 0.015 0 -9999 0 -10000 0 0
YY1 0.034 0 -9999 0 -10000 0 0
HDAC8 0.015 0 -9999 0 -10000 0 0
SMAD7 0.013 0.036 -9999 0 -0.57 1 1
NCOR2 0.015 0 -9999 0 -10000 0 0
MXD1 0.013 0.03 -9999 0 -0.48 1 1
STAT3 0.029 0 -9999 0 -10000 0 0
NFKB1 0.015 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.015 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 0.042 0 -9999 0 -10000 0 0
YY1/SAP30/HDAC1 0.042 0 -9999 0 -10000 0 0
EP300 0.015 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.029 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.025 0.032 -9999 0 -10000 0 0
histone deacetylation 0.054 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.041 0.026 -9999 0 -10000 0 0
nuclear export -0.03 0 -9999 0 -10000 0 0
PRKACA 0.015 0 -9999 0 -10000 0 0
GATAD2B 0.015 0 -9999 0 -10000 0 0
GATAD2A 0.015 0 -9999 0 -10000 0 0
GATA2/HDAC3 0.017 0.067 -9999 0 -0.29 5 5
GATA1/HDAC1 0.019 0.005 -9999 0 -10000 0 0
GATA1/HDAC3 0.02 0.031 -9999 0 -10000 0 0
CHD4 0.015 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A 0.005 0.077 -9999 0 -0.34 13 13
SIN3/HDAC complex/Mad/Max 0.054 0.005 -9999 0 -10000 0 0
NuRD Complex 0.063 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.003 0.015 -9999 0 -10000 0 0
SIN3B 0.015 0 -9999 0 -10000 0 0
MTA2 0.015 0 -9999 0 -10000 0 0
SIN3A 0.015 0 -9999 0 -10000 0 0
XPO1 0.015 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.035 0 -9999 0 -10000 0 0
HDAC complex 0.039 0 -9999 0 -10000 0 0
GATA1/Fog1 0.019 0.005 -9999 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.031 0 -9999 0 -10000 0 0
TNF -0.009 0.11 -9999 0 -0.48 13 13
negative regulation of cell growth 0.053 0.005 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.054 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.038 0 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha 0.041 0.033 -9999 0 -10000 0 0
SIN3/HDAC complex/NCoR1 0.052 0 -9999 0 -10000 0 0
TFCP2 0.015 0 -9999 0 -10000 0 0
NR2C1 0.015 0 -9999 0 -10000 0 0
MBD3 0.015 0 -9999 0 -10000 0 0
MBD2 0.015 0 -9999 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

Figure S129.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S129.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.015 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
MDM2/SUMO1 0.027 0.043 -9999 0 -0.22 8 8
HDAC4 0.015 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
SUMO1 0.015 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.019 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.032 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.015 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.015 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0.035 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.035 0 -9999 0 -10000 0 0
RANGAP1 0.015 0 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.031 0.047 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.025 0 -9999 0 -10000 0 0
Ran/GTP 0.031 0 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0 0.085 -9999 0 -0.48 8 8
UBE2I 0.015 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.037 0 -9999 0 -10000 0 0
NPC 0.009 0 -9999 0 -10000 0 0
PIAS2 0.015 0 -9999 0 -10000 0 0
PIAS1 0.015 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Arf1 pathway

Figure S130.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S130.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0 0 -9999 0 -10000 0 0
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.023 0 -9999 0 -10000 0 0
AP2 0.022 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0 -9999 0 -10000 0 0
CLTB 0.015 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.029 0 -9999 0 -10000 0 0
CD4 0.011 0.05 -9999 0 -0.57 2 2
CLTA 0.015 0 -9999 0 -10000 0 0
mol:GTP 0.002 0 -9999 0 -10000 0 0
ARFGAP1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
ARF1/GTP 0 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.031 0 -9999 0 -10000 0 0
mol:Choline 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.015 0 -9999 0 -10000 0 0
DDEF1 0 0 -9999 0 -10000 0 0
ARF1/GDP 0 0 -9999 0 -10000 0 0
AP2M1 0.015 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0.019 0 -9999 0 -10000 0 0
Rac/GTP 0.013 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.029 0 -9999 0 -10000 0 0
ARFIP2 0.013 0 -9999 0 -10000 0 0
COPA 0.015 0 -9999 0 -10000 0 0
RAC1 0.015 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.029 0 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0 -9999 0 -10000 0 0
GGA3 0.015 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0.021 0 -9999 0 -10000 0 0
AP2A1 0.015 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.031 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0.021 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0 -9999 0 -10000 0 0
CYTH2 0.015 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0 0 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0.011 0 -9999 0 -10000 0 0
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.038 0.021 -9999 0 -10000 0 0
PLD2 0 0 -9999 0 -10000 0 0
ARF-GAP1/v-SNARE 0.013 0 -9999 0 -10000 0 0
PIP5K1A 0 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0 0 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.013 0 -9999 0 -10000 0 0
GOSR2 0 0 -9999 0 -10000 0 0
USO1 0 0 -9999 0 -10000 0 0
GBF1 0 0 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.028 0.032 -9999 0 -0.34 2 2
Alternative NF-kappaB pathway

Figure S131.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S131.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.022 0 -9999 0 -9999 0 0
FBXW11 0.015 0 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.015 0 -9999 0 -9999 0 0
CHUK 0.015 0 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.045 0 -9999 0 -9999 0 0
NFKB1 0.015 0 -9999 0 -9999 0 0
MAP3K14 0.015 0 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.022 0 -9999 0 -9999 0 0
RELB 0.015 0 -9999 0 -9999 0 0
NFKB2 0.015 0 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.021 0 -9999 0 -9999 0 0
regulation of B cell activation 0.02 0 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 267 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.YC.A89H TCGA.XF.A8HG TCGA.XF.A8HF TCGA.XF.A8HE
109_MAP3K5 0.061 -0.2 0.061 0.061
47_PPARGC1A -0.57 -0.57 -0.57 0.015
105_BMP4 0.015 0.015 0.015 0.015
105_BMP6 0.015 0.015 0.015 0.015
105_BMP7 0.015 -0.57 -0.57 -0.57
105_BMP2 0.015 0.015 0.015 0.015
131_RELN/VLDLR -0.3 0.039 -0.3 -0.24
30_TGFB1/TGF beta receptor Type II 0.018 0.014 0.015 0.018
84_STAT5B 0.05 0.0066 0.014 0.051
84_STAT5A 0.05 0.0066 0.014 0.051
Methods & Data
Input

  • Expression Data Normalization = Normal controls were used to median center the expression data used in this analysis.

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/BLCA-TP/9827962/BLCA-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = Copy number data was not used in this analysis.

Data Sets and Pathway Interactions

Both copy number and expression data are incorporated into PARADIGM's inference. Whenever normal tissue controls are available for analysis in the expression data, each patient's gene-value is normalized by subtracting the gene's median level observed in the normal control. Copy number data is also normalized to reflect the difference in copy number between a gene's levels detected in tumor versus control (e.g. blood normal). The collection of pathways used by PARADIGM includes those from NCI-PID on September 15, 2009 containing 131 pathways, 11,563 interactions, and 7,204 entities. All gene identifiers were translated into HUGO standard identifiers wherever possible. We refer to molecular entities as "concepts," which include gene products such as proteins and miRNAs, small molecules, protein complexes, and abstract concepts. Each concept is represented as "node" in PARADIGM's graphical model. The abstract concepts correspond to general cellular processes (such as "apoptosis" or "DNA damage response") and families of genes that share functional activity such as the RAS family of signal transducers. Various types of concept-concept interactions are included in the pathways including protein-protein interactions, transcriptional regulatory interactions, and protein modifications such as phosphorylation and ubiquitinylation interactions.

Pathway Inference Method

The PARADIGM algorithm (described in PMID: 20529912) assigns an integrated pathway level (IPL) reflecting the activity of a concept determined through a belief propagation strategy. The belief propagation is given the copy number and gene expression measurements of all of the genes and iteratively updates hidden states reflecting the activities of all of the genes in a pathway so as to maximize the likelihood of the observed data given the interactions in the pathway. In the end, the inferred level of a concept reflects both the data observed for the concept and the neighborhood of activity surrounding the concept.

Determining significantly altered levels

The significance of the IPL obtained for each concept in each patient sample is assessed using a permutation analysis. Importantly, the permutation analysis preserves data tuples so as to preserve any implicit correlations between the different data modalities. For example, genes that are deleted have concomitantly lower expression levels. Preserving the copy number and expression pairs therefore retains this data property. The simulation therefore makes "null samples" by permuting data tuples across all of the genes in the genome so that each gene in a null sample is associated with a random tuple of another gene with equal probability. This approach has the added benefit of preserving the pathway structure so that every observed IPL can be compared to a distribution of random IPLs derived from exactly the same interaction context. PARADIGM inferences are then obtained for 1000 "null" patients and serve as a background distribution to contrast the observed IPLs against. Pathway concepts are excluded from further analysis if they did not obtain a minimum IPL of 0.5 in any patient sample both observed or simulated.

An IPL I(i,j) for concept i in sample j, is considered to be deviated if its absolute level is two standard deviations from the average level observed for concept i in the 1000 null samples. The degree to which a concept has significantly altered levels across a patient cohort is summarized in the proportion of deviated samples (PDS) score. For example, a protein with a PDS of 0.10 reflects that the protein's level of activity was inferred to be significantly higher or lower in tumors compared to normal in 10% of the patient samples. An average PDS for a pathway is also reported by computing the mean PDS over all concepts in the pathway.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[2] Charles J. Vaske, Stephen C. Benz, J. Zachary Sanborn, Dent Earl, Christopher Szeto, Jingchun Zhu, David Haussler, and Joshua M. Stuart, Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM, Bioinformatics 12(26):237-245 (2010)
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